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= 024258
(270 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 = 99.8 bits (247), Expect = 1e-21, Method: Compositional matrix adjust.
Identities = 49/92 (53%), Positives = 68/92 (73%), Gaps = 1/92 (1%)
Query: 4 FGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
+GR PPD+ SL V N+T+RT+ D L +F+KYG+V D++IPRDR T +SRGFAFVR
Sbjct: 37 YGRP-PPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVR 95
Query: 64 YKYADEAQKAVDRLDGRVVDGREITVQFAKYG 95
+ +A+ A+D +DG V+DGRE+ VQ A+YG
Sbjct: 96 FHDKRDAEDAMDAMDGAVLDGRELRVQMARYG 127
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 45/85 (52%), Positives = 63/85 (74%)
Query: 11 DITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEA 70
D+ SL V N+T+RT+ D L +F+KYG+V D++IPRDR T +SRGFAFVR+ +A
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 71 QKAVDRLDGRVVDGREITVQFAKYG 95
+ A+D +DG V+DGRE+ VQ A+YG
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYG 150
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 82.0 bits (201), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 44/91 (48%), Positives = 61/91 (67%), Gaps = 1/91 (1%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G SGP D+ +L V N+T+RT+ D L +F+KYG+V D++IPR+ T RGFAFVR+
Sbjct: 4 GSSGP-DVDGMITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRF 62
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQFAKYG 95
+AQ A +DG +DGRE+ VQ A+YG
Sbjct: 63 HDRRDAQDAEAAMDGAELDGRELRVQVARYG 93
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 63.2 bits (152), Expect = 1e-10, Method: Compositional matrix adjust.
Identities = 35/90 (38%), Positives = 52/90 (57%), Gaps = 2/90 (2%)
Query: 3 HFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFV 62
H G PD L V ++ TT DL +F KYG + D+ I D+++ SRGFAFV
Sbjct: 36 HVGNRANPD--PNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFV 93
Query: 63 RYKYADEAQKAVDRLDGRVVDGREITVQFA 92
++ D+A++A +R +G +DGR I V F+
Sbjct: 94 YFENVDDAKEAKERANGMELDGRRIRVDFS 123
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 32/86 (37%), Positives = 51/86 (59%), Gaps = 1/86 (1%)
Query: 13 TDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
+D L V ++F T L +F KYG++ ++ + +DR T SRGF FV ++ D+A+
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 73 AVDRLDGRVVDGREITV-QFAKYGPN 97
A+ ++G+ VDGR+I V Q K N
Sbjct: 70 AMMAMNGKSVDGRQIRVDQAGKSSDN 95
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 48/75 (64%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V ++ TT DL +F KYG + D+ I D+++ SRGFAFV ++ D+A++A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 78 DGRVVDGREITVQFA 92
+G +DGR I V F+
Sbjct: 78 NGMELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 48/76 (63%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
L V ++ TT DL +F KYG + D+ I D+++ SRGFAFV ++ D+A++A +R
Sbjct: 14 CLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKER 73
Query: 77 LDGRVVDGREITVQFA 92
+G +DGR I V F+
Sbjct: 74 ANGMELDGRRIRVDFS 89
>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 = 58.5 bits (140), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 4 FGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
+ R G I DT +L V N+ T D L +F KYG +V I RD+ TG RG AFVR
Sbjct: 3 YARPGGESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 61
Query: 64 YKYADEAQKAVDRLDGRVVDG 84
Y +EAQ+A+ L+ + +G
Sbjct: 62 YNKREEAQEAISALNNVIPEG 82
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 58.2 bits (139), Expect = 5e-09, Method: Compositional matrix adjust.
Identities = 30/73 (41%), Positives = 46/73 (63%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V ++ TT DL +F KYG + D+ I D+++ SRGFAFV ++ D+A++A +R
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 78 DGRVVDGREITVQ 90
+G +DGR I V
Sbjct: 78 NGMELDGRRIRVS 90
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 57.4 bits (137), Expect = 8e-09, Method: Compositional matrix adjust.
Identities = 34/82 (41%), Positives = 46/82 (56%), Gaps = 1/82 (1%)
Query: 3 HFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFV 62
+ R G I DT +L V N+ T D L +F KYG +V I RD+ TG RG AFV
Sbjct: 78 SYARPGGESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFV 136
Query: 63 RYKYADEAQKAVDRLDGRVVDG 84
RY +EAQ+A+ L+ + +G
Sbjct: 137 RYNKREEAQEAISALNNVIPEG 158
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 42/76 (55%), Gaps = 2/76 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T +L+ LF G + I RD +TG S G+AFV + ++Q+A+ L+G V + +
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 88 TVQFAKYGPNAERIKE 103
V +A+ P E IK+
Sbjct: 76 KVSYAR--PGGESIKD 89
>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 = 57.4 bits (137), Expect = 9e-09, Method: Composition-based stats.
Identities = 31/77 (40%), Positives = 44/77 (57%), Gaps = 4/77 (5%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D V +++ T+ DL F K+G+VVD I D TG SRGF F+ +K A +K
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV 69
Query: 74 VD----RLDGRVVDGRE 86
+D RLDGRV+D ++
Sbjct: 70 LDQKEHRLDGRVIDPKK 86
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 44/83 (53%), Gaps = 3/83 (3%)
Query: 13 TDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGD---SRGFAFVRYKYADE 69
+ + L + N+ F TT + L +F K G + I + + S GF FV YK ++
Sbjct: 3 SGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 70 AQKAVDRLDGRVVDGREITVQFA 92
AQKA+ +L G VDG ++ V+ +
Sbjct: 63 AQKALKQLQGHTVDGHKLEVRIS 85
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 34/81 (41%), Positives = 46/81 (56%), Gaps = 1/81 (1%)
Query: 4 FGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
+ R G I DT +L V N+ T D L +F KYG +V I RD+ TG RG AFVR
Sbjct: 90 YARPGGESIKDT-NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVR 148
Query: 64 YKYADEAQKAVDRLDGRVVDG 84
Y +EAQ+A+ L+ + +G
Sbjct: 149 YNKREEAQEAISALNNVIPEG 169
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T +L+ LF G + I RD +TG S G+AFV + ++Q+A+ L+G V + +
Sbjct: 27 TDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITVRNKRL 86
Query: 88 TVQFAKYGPNAERIKEGLL 106
V +A+ P E IK+ L
Sbjct: 87 KVSYAR--PGGESIKDTNL 103
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 42/72 (58%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+++ ++ +DL LF YG + ++ P D T +GFAFV + + + A KA +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 78 DGRVVDGREITV 89
DG+V GR + V
Sbjct: 71 DGQVFQGRMLHV 82
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 48/85 (56%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V + T +D+ F +YG++ +I + DRRTG +G+ V Y+
Sbjct: 2 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 61
Query: 68 DEAQKAVDRLDGRVVDGREITVQFA 92
EAQ A++ L+G+ + G+ I+V +
Sbjct: 62 KEAQAAMEGLNGQDLMGQPISVDWC 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 = 54.3 bits (129), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 48/85 (56%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V + T +D+ F +YG++ +I + DRRTG +G+ V Y+
Sbjct: 16 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 75
Query: 68 DEAQKAVDRLDGRVVDGREITVQFA 92
EAQ A++ L+G+ + G+ I+V +
Sbjct: 76 KEAQAAMEGLNGQDLMGQPISVDWC 100
>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 = 54.3 bits (129), Expect = 7e-08, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 48/85 (56%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V + T +D+ F +YG++ +I + DRRTG +G+ V Y+
Sbjct: 15 GPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETY 74
Query: 68 DEAQKAVDRLDGRVVDGREITVQFA 92
EAQ A++ L+G+ + G+ I+V +
Sbjct: 75 KEAQAAMEGLNGQDLMGQPISVDWC 99
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 47/84 (55%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + + L V + T +D+ F +YG++ +I + DRRTG +G+ V Y+
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 69 EAQKAVDRLDGRVVDGREITVQFA 92
EAQ A++ L+G+ + G+ I+V +
Sbjct: 61 EAQAAMEGLNGQDLMGQPISVDWC 84
>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 = 53.1 bits (126), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 26/84 (30%), Positives = 47/84 (55%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + + L V + T +D+ F +YG++ +I + DRRTG +G+ V Y+
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 69 EAQKAVDRLDGRVVDGREITVQFA 92
EAQ A++ L+G+ + G+ I+V +
Sbjct: 61 EAQAAMEGLNGQDLMGQPISVDWC 84
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 53.1 bits (126), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
++ V N+ F T +DL+ +F KYGKVV + I +D+ T S+G AF+ + D AQ
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 77 LDGRVVDGREITVQFA 92
++ + + GR I A
Sbjct: 78 INNKQLFGRVIKASIA 93
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 52.4 bits (124), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 2/75 (2%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V NI FR DL +F ++GK++D+ I + R S+GF FV ++ + +A +A ++L
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG--SKGFGFVTFENSADADRAREKL 89
Query: 78 DGRVVDGREITVQFA 92
G VV+GR+I V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 52.4 bits (124), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/86 (33%), Positives = 43/86 (50%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
S+ V NI + T + L +F + G VV + DR TG +G+ F Y+ + A A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 77 LDGRVVDGREITVQFAKYGPNAERIK 102
L+GR GR + V A N E +K
Sbjct: 70 LNGREFSGRALRVDNAASEKNKEELK 95
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 52.0 bits (123), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 47/75 (62%), Gaps = 2/75 (2%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V NI FR DL +F ++GK++D+ I + R S+GF FV ++ + +A +A ++L
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREKL 75
Query: 78 DGRVVDGREITVQFA 92
G VV+GR+I V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 51.6 bits (122), Expect = 4e-07, Method: Composition-based stats.
Identities = 26/67 (38%), Positives = 42/67 (62%), Gaps = 1/67 (1%)
Query: 23 ITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGD-SRGFAFVRYKYADEAQKAVDRLDGRV 81
+T T D + +F YGK+ I +P +R S+G+A+V ++ DEA+KA+ +DG
Sbjct: 12 LTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQ 71
Query: 82 VDGREIT 88
+DG+EIT
Sbjct: 72 IDGQEIT 78
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 52/95 (54%), Gaps = 1/95 (1%)
Query: 5 GRSGPPD-ITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
G SGP D ++ V N++ T DL LF +G + I++ +D+ TG S+GFAF+
Sbjct: 4 GSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFIS 63
Query: 64 YKYADEAQKAVDRLDGRVVDGREITVQFAKYGPNA 98
+ ++A +A+ + G D + V++AK N+
Sbjct: 64 FHRREDAARAIAGVSGFGYDHLILNVEWAKPSTNS 98
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 48/95 (50%), Gaps = 6/95 (6%)
Query: 1 MSHFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFA 60
+ F + G T L V N+ T +D LF++YG+ ++FI RD RGF
Sbjct: 8 IKSFLKPGEKTYTQRCRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFG 61
Query: 61 FVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYG 95
F+R + A+ A LDG ++ R + ++FA +G
Sbjct: 62 FIRLESRTLAEIAKAELDGTILKSRPLRIRFATHG 96
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V +I D++ F YG++ +I + DRRTG S+G+A V Y+
Sbjct: 19 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 78
Query: 68 DEAQKAVDRLDGRVVDGREITVQFA 92
+A A + L+G + G+ I V +
Sbjct: 79 KQALAAKEALNGAEIMGQTIQVDWC 103
>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 = 51.2 bits (121), Expect = 6e-07, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 42/70 (60%), Gaps = 4/70 (5%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD-- 75
+ + +++ TT DL F K+G+VVD + D TG SRGF FV +K ++ K +D
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 76 --RLDGRVVD 83
+L+G+V+D
Sbjct: 62 EHKLNGKVID 71
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 44/77 (57%), Gaps = 3/77 (3%)
Query: 12 ITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQ 71
+ T L+VL + ++TT DL F +G+V+ + + +D +TG S+GF FVR+ +
Sbjct: 12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQV 71
Query: 72 KAVDR---LDGRVVDGR 85
K + + +DGR D +
Sbjct: 72 KVMSQRHMIDGRWCDCK 88
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 51.2 bits (121), Expect = 6e-07, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 47/83 (56%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + + L V + T +D+ F +YG++ +I + DRRTG +G+ V Y+
Sbjct: 1 PQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYK 60
Query: 69 EAQKAVDRLDGRVVDGREITVQF 91
EAQ A++ L+G+ + G+ I+V +
Sbjct: 61 EAQAAMEGLNGQDLMGQPISVDW 83
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 50.8 bits (120), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L V + + TT L F+ YG + I + +R+G RG+AF+ Y++ + A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 77 LDGRVVDGREITV 89
DG+ +DGR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+G + + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 88 TVQFAKYGPNAERIKEGLL 106
V +A+ P++E IK+ L
Sbjct: 75 KVSYAR--PSSEVIKDANL 91
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 39/67 (58%), Gaps = 2/67 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGRE- 86
T D+ +F ++G++++ + D+ TG SRG AF+R+ EA++A+ +G G
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSE 160
Query: 87 -ITVQFA 92
ITV FA
Sbjct: 161 PITVXFA 167
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 46/79 (58%), Gaps = 2/79 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+G + + I
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 88 TVQFAKYGPNAERIKEGLL 106
V +A+ P++E IK+ L
Sbjct: 75 KVSYAR--PSSEVIKDANL 91
Score = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 40/67 (59%), Gaps = 2/67 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGRE- 86
T D+ +F ++G++++ + D+ TG SRG AF+R+ EA++A+ +G G
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNGHKPPGSSE 160
Query: 87 -ITVQFA 92
ITV+FA
Sbjct: 161 PITVKFA 167
>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 = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 39/73 (53%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L V + + TT L F+ YG + I + +R+G RG+AF+ Y++ + A
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKH 163
Query: 77 LDGRVVDGREITV 89
DG+ +DGR + V
Sbjct: 164 ADGKKIDGRRVLV 176
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 48/88 (54%)
Query: 11 DITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEA 70
D ++ + + V +++ T +D+ F +GK+ D + +D TG S+G+ FV + +A
Sbjct: 11 DTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDA 70
Query: 71 QKAVDRLDGRVVDGREITVQFAKYGPNA 98
+ A+ + G+ + GR+I +A P A
Sbjct: 71 ENAIVHMGGQWLGGRQIRTNWATRKPPA 98
>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 = 49.7 bits (117), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/97 (26%), Positives = 53/97 (54%), Gaps = 1/97 (1%)
Query: 5 GRSG-PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
G SG D ++ + + V +++ T +D+ F +G++ D + +D TG S+G+ FV
Sbjct: 4 GSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVS 63
Query: 64 YKYADEAQKAVDRLDGRVVDGREITVQFAKYGPNAER 100
+ +A+ A+ ++ G+ + GR+I +A P A +
Sbjct: 64 FFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPK 100
>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 = 49.3 bits (116), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 45/85 (52%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
GP + + L V +I D++ F YG++ +I + DRRTG S+G+A V Y+
Sbjct: 65 GPQRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETH 124
Query: 68 DEAQKAVDRLDGRVVDGREITVQFA 92
+A A + L+G + G+ I V +
Sbjct: 125 KQALAAKEALNGAEIMGQTIQVDWC 149
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 48.9 bits (115), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 44/90 (48%), Gaps = 1/90 (1%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADD-LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
G SG + T +L + D L F +G + DI IP D T RGFAFV
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 64 YKYADEAQKAVDRLDGRVVDGREITVQFAK 93
++ A++A A+D ++ + GR I V AK
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 54/99 (54%), Gaps = 15/99 (15%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G SG +T+ + V N++ T+ +L LF++ G+V++ + +D +AFV
Sbjct: 1 GSSGSSG--NTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHM 50
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQFA-----KYGPNA 98
+ +A+ A+ +L+G+ V G+ I V+ + K GP++
Sbjct: 51 EKEADAKAAIAQLNGKEVKGKRINVELSTKGQKKSGPSS 89
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 40/75 (53%), Gaps = 4/75 (5%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV--- 74
L V + + TT + L F +YG+VVD I +D+ T SRGF FV++K + +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLASR 78
Query: 75 -DRLDGRVVDGREIT 88
LDGR +D + T
Sbjct: 79 PHTLDGRNIDPKPCT 93
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L F+++G + D + RD T SRGF FV Y +
Sbjct: 8 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
Query: 69 EAQKAVD----RLDGRVVD 83
E A++ ++DGRVV+
Sbjct: 68 EVDAAMNARPHKVDGRVVE 86
Score = 36.2 bits (82), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L F++YGK+ I I DR +G RGFAFV + D K V
Sbjct: 108 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L F+++G + D + RD T SRGF FV Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 69 EAQKAVD----RLDGRVVD 83
E A++ ++DGRVV+
Sbjct: 67 EVDAAMNARPHKVDGRVVE 85
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L F++YGK+ I I DR +G RGFAFV + D K V
Sbjct: 107 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L F+++G + D + RD T SRGF FV Y +
Sbjct: 6 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
Query: 69 EAQKAVD----RLDGRVVD 83
E A++ ++DGRVV+
Sbjct: 66 EVDAAMNARPHKVDGRVVE 84
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 28/57 (49%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L F++YGK+ I I DR +G RGFAFV + D K V
Sbjct: 106 IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>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 = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD- 75
L + ++F TT + L F+++G + D + RD T SRGF FV Y +E A++
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 76 ---RLDGRVVD 83
++DGRVV+
Sbjct: 68 RPHKVDGRVVE 78
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 28/58 (48%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L F++YGK+ I I DR +G RGFAFV + D K V
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 49/95 (51%), Gaps = 6/95 (6%)
Query: 1 MSHFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFA 60
+ +F + G T L V N+ T +++ LF+KYGK ++FI +D +GF
Sbjct: 8 LKNFRKPGEKTFTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFG 61
Query: 61 FVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYG 95
F+R + A+ A LD + G+++ V+FA +
Sbjct: 62 FIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHS 96
>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 = 5e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 3/73 (4%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKY---ADEA 70
++ + + + + TT D+L F KYG V D+ I +D TG SRGF F+ ++ DE
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 71 QKAVDRLDGRVVD 83
K LDG+V+D
Sbjct: 62 VKTQHILDGKVID 74
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 35 LFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL-DGRVVDGREITVQFAK 93
F ++G ++D + D+ TG SRGF FV Y AD AVDR+ + +D ++ ++ +
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD----AVDRVCQNKFIDFKDRKIEIKR 162
Query: 94 YGP 96
P
Sbjct: 163 AEP 165
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L F+++G + D + RD T SRGF FV Y +
Sbjct: 7 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
Query: 69 EAQKAVD----RLDGRVVD 83
E A++ ++DGRVV+
Sbjct: 67 EVDAAMNARPHKVDGRVVE 85
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 28/58 (48%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L F++YGK+ I I DR +G RGFAFV + D K V
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 48.1 bits (113), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 35/62 (56%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQF 91
L F +G + DI IP D T RGFAFV ++ A++A A+D ++ + GR I V
Sbjct: 24 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 83
Query: 92 AK 93
AK
Sbjct: 84 AK 85
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 4/79 (5%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P + L + ++F TT + L F+++G + D + RD T SRGF FV Y +
Sbjct: 5 PKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
Query: 69 EAQKAVD----RLDGRVVD 83
E A++ ++DGRVV+
Sbjct: 65 EVDAAMNARPHKVDGRVVE 83
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 28/58 (48%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
+ V I T L F++YGK+ I I DR +G RGFAFV + D K V
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 25/62 (40%), Positives = 35/62 (56%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQF 91
L F +G + DI IP D T RGFAFV ++ A++A A+D ++ + GR I V
Sbjct: 22 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 81
Query: 92 AK 93
AK
Sbjct: 82 AK 83
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%)
Query: 6 RSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
+S DT++L V ++ + L F + + + D +TG SRG+ FV +
Sbjct: 78 QSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFT 137
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFA 92
D+AQ A+D + G+ ++GR + + +A
Sbjct: 138 SQDDAQNAMDSMQGQDLNGRPLRINWA 164
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 20/75 (26%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T D L F G + +I I D+ + +AFV Y + +A A+ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVN-YAFVEYHQSHDANIALQTL 61
Query: 78 DGRVVDGREITVQFA 92
+G+ ++ + + +A
Sbjct: 62 NGKQIENNIVKINWA 76
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 48/77 (62%)
Query: 13 TDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
+ + L V ++ F T D L +F+ +GK+ +I + +D TG S+G+ F+ + ++ A++
Sbjct: 3 SGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARR 62
Query: 73 AVDRLDGRVVDGREITV 89
A+++L+G + GR + V
Sbjct: 63 ALEQLNGFELAGRPMRV 79
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 40/71 (56%), Gaps = 2/71 (2%)
Query: 27 TTADD--LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDG 84
TT D+ L LF++YG + + I DR T SRG+ FV+++ AQ+A+ L+G +
Sbjct: 52 TTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNGFNILN 111
Query: 85 REITVQFAKYG 95
+ + V A G
Sbjct: 112 KRLKVALAASG 122
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQF 91
L F +G + DI IP D T RGFAFV ++ A++A A+D ++ + GR I V
Sbjct: 80 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 139
Query: 92 A 92
A
Sbjct: 140 A 140
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 44/72 (61%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V ++ F T D L +F+ +G++ I + D TG S+G+ F+ + ++ A+KA+++L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 78 DGRVVDGREITV 89
+G + GR + V
Sbjct: 89 NGFELAGRPMKV 100
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/66 (34%), Positives = 38/66 (57%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T D+L LF G+V + RD+ G S G+ FV Y A +A++A++ L+G + + I
Sbjct: 32 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 91
Query: 88 TVQFAK 93
V +A+
Sbjct: 92 KVSYAR 97
>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 = 46.6 bits (109), Expect = 1e-05, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 43/77 (55%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L+V + T D+L LF G+V + RD+ G S G+ FV Y A +A++A++
Sbjct: 6 NLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINT 65
Query: 77 LDGRVVDGREITVQFAK 93
L+G + + I V +A+
Sbjct: 66 LNGLRLQSKTIKVSYAR 82
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 46.6 bits (109), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 49/90 (54%), Gaps = 3/90 (3%)
Query: 14 DTYSLLVLN-ITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
D+ + L++N + T D+ LF G + + RD+ TG S G+ FV Y ++A K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 73 AVDRLDGRVVDGREITVQFAKYGPNAERIK 102
A++ L+G + + I V +A+ P++ I+
Sbjct: 62 AINTLNGLKLQTKTIKVSYAR--PSSASIR 89
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/94 (29%), Positives = 51/94 (54%), Gaps = 3/94 (3%)
Query: 14 DTYSLLVLN-ITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
D+ + L++N + T D+ LF G + + RD+ TG S G+ FV Y ++A K
Sbjct: 2 DSKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADK 61
Query: 73 AVDRLDGRVVDGREITVQFAKYGPNAERIKEGLL 106
A++ L+G + + I V +A+ P++ I++ L
Sbjct: 62 AINTLNGLKLQTKTIKVSYAR--PSSASIRDANL 93
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 48/92 (52%), Gaps = 3/92 (3%)
Query: 3 HFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFV 62
+ R I D +L V + + ++ LF +YG+++ I D+ TG SRG F+
Sbjct: 79 SYARPSSASIRDA-NLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFI 137
Query: 63 RYKYADEAQKAVDRLDGRVVDG--REITVQFA 92
R+ EA++A+ L+G+ G ITV+FA
Sbjct: 138 RFDKRIEAEEAIKGLNGQKPLGAAEPITVKFA 169
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 43/76 (56%), Gaps = 1/76 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L + + T L +F K+G + ++ + +DR T SRGFAF+ ++ +A+ A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 78 DGRVVDGREITVQFAK 93
+G+ + G+ I V+ AK
Sbjct: 69 NGKSLHGKAIKVEQAK 84
>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 = 46.2 bits (108), Expect = 2e-05, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 42/78 (53%)
Query: 15 TYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
T++L V ++ + L F + + + D +TG SRG+ FV + D+AQ A+
Sbjct: 1 TFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAM 60
Query: 75 DRLDGRVVDGREITVQFA 92
D + G+ ++GR + + +A
Sbjct: 61 DSMQGQDLNGRPLRINWA 78
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 45.8 bits (107), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 46/86 (53%), Gaps = 5/86 (5%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV--- 74
L + ++F TT + L ++++GK+ D + RD + SRGF FV + E A+
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAAR 89
Query: 75 -DRLDGRVVD-GREITVQFAKYGPNA 98
+DGRVV+ R + + + GP++
Sbjct: 90 PHSIDGRVVEPKRAVAREESGSGPSS 115
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 45.8 bits (107), Expect = 2e-05, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 2/75 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T +L+ LF G + I RD +TG S G+AFV + ++Q+A+ L+G V + +
Sbjct: 16 TDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRNKRL 75
Query: 88 TVQFAKYGPNAERIK 102
V +A+ P E IK
Sbjct: 76 KVSYAR--PGGESIK 88
>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 = 45.8 bits (107), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 34/61 (55%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQF 91
L F +G + DI IP D T RGFAFV ++ A++A A+D ++ + GR I V
Sbjct: 19 LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNL 78
Query: 92 A 92
A
Sbjct: 79 A 79
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 48/92 (52%), Gaps = 3/92 (3%)
Query: 3 HFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFV 62
+ R I D +L V + T +L LF +YG+++ I D+ TG SRG F+
Sbjct: 77 SYARPSSASIRDA-NLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFI 135
Query: 63 RYKYADEAQKAVDRLDGRVVDG--REITVQFA 92
R+ EA++A+ L+G+ G ITV+FA
Sbjct: 136 RFDKRIEAEEAIKGLNGQKPSGATEPITVKFA 167
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
T ++ LF G++ + RD+ TG S G+ FV Y +A+KA++ L+G + + I
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 88 TVQFAKYGPNAERIKEGLL 106
V +A+ P++ I++ L
Sbjct: 75 KVSYAR--PSSASIRDANL 91
>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 = 44.7 bits (104), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
+ + L + + F T ++L + +G V D+ + +R G +G A+V Y+ +A +A
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQA 74
Query: 74 VDRLDGRVVDGREITVQFAKYGPNA 98
V ++DG + I V + GP++
Sbjct: 75 VMKMDGMTIKENIIKVAISNSGPSS 99
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 44.7 bits (104), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 48/90 (53%), Gaps = 4/90 (4%)
Query: 5 GRSGPPDITD-TYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
G SGP + + +L V ++ TT + L FD V I DR TG S+GF FV
Sbjct: 4 GSSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVD 60
Query: 64 YKYADEAQKAVDRLDGRVVDGREITVQFAK 93
+ ++A+ A + ++ +DG ++T+ +AK
Sbjct: 61 FNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 50/92 (54%), Gaps = 9/92 (9%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L + N+ ++ TA++++ +F KYG + I R T ++RG A+V Y+
Sbjct: 4 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 58
Query: 69 EAQKAVDRLDGRVVDGREITVQFAKYGPNAER 100
+A+ AVD L G V R + V + NA R
Sbjct: 59 DAKNAVDHLSGFNVSNRYLVVLYY----NANR 86
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 49/77 (63%), Gaps = 4/77 (5%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
++ +L++ N+++ T + L +F+K I +P+++ G S+G+AF+ + ++A++A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQ-NGKSKGYAFIEFASFEDAKEA 69
Query: 74 VDRLDGRVVDGREITVQ 90
++ + R ++GR I ++
Sbjct: 70 LNSCNKREIEGRAIRLE 86
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L + N+ ++ TA++++ +F KYG + I R T ++RG A+V Y+
Sbjct: 8 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 62
Query: 69 EAQKAVDRLDGRVVDGREITVQF 91
+A+ A D L G V R + V +
Sbjct: 63 DAKNACDHLSGFNVCNRYLVVLY 85
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 47/83 (56%), Gaps = 5/83 (6%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L++ N+ ++ TA++++ +F KYG + I R T ++RG A+V Y+
Sbjct: 14 PPEVNRI--LMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 68
Query: 69 EAQKAVDRLDGRVVDGREITVQF 91
+A+ A D L G V R + V +
Sbjct: 69 DAKNACDHLSGFNVCNRYLVVLY 91
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 6/83 (7%)
Query: 12 ITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQ 71
T L V N+ T +++ LF+KYGK ++FI +D +GF F+R + A+
Sbjct: 12 FTQRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAE 65
Query: 72 KAVDRLDGRVVDGREITVQFAKY 94
A LD + G+++ V+FA +
Sbjct: 66 IAKVELDNMPLRGKQLRVRFACH 88
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G SG D D L + I DL PLF+++GK+ ++ + +DR TG +G AF+ Y
Sbjct: 4 GSSGMKD-HDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 65 KYADEAQKAVDRL 77
+ A KA L
Sbjct: 63 CERESALKAQSAL 75
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 5 GRSG-PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
G SG P D L V I DL PLF+++G++ ++ + +DR TG +G AF+
Sbjct: 4 GSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLT 63
Query: 64 YKYADEAQKAVDRL 77
Y D A KA L
Sbjct: 64 YCARDSALKAQSAL 77
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 42.7 bits (99), Expect = 2e-04, Method: Composition-based stats.
Identities = 24/60 (40%), Positives = 37/60 (61%), Gaps = 2/60 (3%)
Query: 35 LFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDG--REITVQFA 92
LF +YG+++ I D+ TG SRG F+R+ EA++A+ L+G+ G ITV+FA
Sbjct: 21 LFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLNGQKPLGAAEPITVKFA 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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
PP++ L + N+ ++ TA++++ +F KYG + I R T ++RG A+V Y+
Sbjct: 14 PPEVNRI--LYIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIF 68
Query: 69 EAQKAVDRLDGRVVDGREITVQF 91
+A+ A D L G V R + V +
Sbjct: 69 DAKNACDHLSGFNVCNRYLVVLY 91
>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 = 16/49 (32%), Positives = 29/49 (59%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
DD+ +F+ +GK+ + RD TG +G+ F+ Y+ A +Q AV ++
Sbjct: 140 DDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
+ V +I + D + F +G + I + D T +GFAFV Y+ + AQ A++++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 78 DGRVVDGREITV 89
+ ++ GR I V
Sbjct: 91 NSVMLGGRNIKV 102
>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 = 42.4 bits (98), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 29/49 (59%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
DD+ +F+ +GK+ + RD TG +G+ F+ Y+ A +Q AV ++
Sbjct: 125 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
+ V +I + D + F +G + I + D T +GFAFV Y+ + AQ A++++
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 78 DGRVVDGREITV 89
+ ++ GR I V
Sbjct: 76 NSVMLGGRNIKV 87
>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 = 3e-04, Method: Compositional matrix adjust.
Identities = 31/100 (31%), Positives = 49/100 (49%), Gaps = 7/100 (7%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L V N++F TT + ++ LF K G + I + D+ + GF FV Y +A+ A+
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 77 LDGRVVDGREITVQFAKYGPNAERIKEGLLNHSRDRSTGQ 116
++G +D R I + KEG + R RS GQ
Sbjct: 101 INGTRLDDRIIRTDWDA------GFKEG-RQYGRGRSGGQ 133
>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 = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVD 83
L LF K GKVV++ P D TG ++GF FV ++A+K + G+ +D
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 43/78 (55%), Gaps = 5/78 (6%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D +LL N+ ++ T D+L +F+ ++ + +D G S+G A++ +K +A+K
Sbjct: 92 DARTLLAKNLPYKVTQDELKEVFEDAAEIR--LVSKD---GKSKGIAYIEFKTEADAEKT 146
Query: 74 VDRLDGRVVDGREITVQF 91
+ G +DGR I++ +
Sbjct: 147 FEEKQGTEIDGRSISLYY 164
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
++ V N+ + T++ + LF ++GKV ++ + DR T +GF FV + + +A+ +
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAK 61
Query: 77 LDGRVVDGREITV 89
LD GR I V
Sbjct: 62 LDNTDFMGRTIRV 74
>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 = 41.2 bits (95), Expect = 7e-04, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 34/58 (58%)
Query: 39 YGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGP 96
+G++ D + +D TG S+G+ FV + +A+ A+ ++ G+ + GR+I +A P
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKP 87
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 37/62 (59%), Gaps = 1/62 (1%)
Query: 32 LFPLFDKYGKVVDI-FIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQ 90
L+ F +G ++ I RD TG+S+G+AF+ + D + A++ ++G+ + R ITV
Sbjct: 22 LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIEAMNGQYLCNRPITVS 81
Query: 91 FA 92
+A
Sbjct: 82 YA 83
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVD 83
L LF K GKVV++ P D TG ++GF FV ++A+K + G+ +D
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHGKRLD 80
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 44/93 (47%), Gaps = 13/93 (13%)
Query: 5 GRSGPPDITDTYSL----LVLNI-TFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGF 59
G SG TD S+ + N+ T D+ +F KYGK+V + +GF
Sbjct: 1 GSSGSSGKTDPRSMNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGF 52
Query: 60 AFVRYKYADEAQKAVDRLDGRVVDGREITVQFA 92
AFV+Y A+ AV DGR++ G+ + + A
Sbjct: 53 AFVQYVNERNARAAVAGEDGRMIAGQVLDINLA 85
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 44/76 (57%), Gaps = 7/76 (9%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDI-FIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
+LL N++F T D+L +F+ ++I + +D G S+G A++ +K +A+K ++
Sbjct: 18 TLLAKNLSFNITEDELKEVFED---ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLE 71
Query: 76 RLDGRVVDGREITVQF 91
G +DGR +++ +
Sbjct: 72 EKQGAEIDGRSVSLYY 87
>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 = 16/49 (32%), Positives = 28/49 (57%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLD 78
DD+ +F+ +GK+ + RD TG +G+ F+ Y+ A +Q AV +
Sbjct: 124 DDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Score = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
+ V +I + D + F +G + I D T +GFAFV Y+ + AQ A+++
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 78 DGRVVDGREITV 89
+ + GR I V
Sbjct: 75 NSVXLGGRNIKV 86
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 35/62 (56%), Gaps = 1/62 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + + + DD+ LF+ +G + + I R G+S+G AFV+Y EAQ A++ L
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-DGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 78 DG 79
G
Sbjct: 77 HG 78
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L + +F ++G+++DI + R + RG AFV +K
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFK 60
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 42/88 (47%), Gaps = 1/88 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
+ V + + TT L F+ +G + + + DR+TG SRG+ FV A++A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 78 DGRVVDGREITVQFAKYGPNAERIKEGL 105
+ ++DGR+ V A G ++ G
Sbjct: 80 N-PIIDGRKANVNLAYLGAKPRSLQTGF 106
>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 = 21/61 (34%), Positives = 35/61 (57%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQF 91
L+ LF + G VV+ +P+DR TG +G+ FV + ++A A+ +D + G+ I V
Sbjct: 32 LWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNK 91
Query: 92 A 92
A
Sbjct: 92 A 92
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/103 (30%), Positives = 48/103 (46%), Gaps = 13/103 (12%)
Query: 5 GRSGPPD-ITDTYSLLVLNITFRTTADDLFPLFDKYGKV----------VDIFIPRDRRT 53
G SG PD +D ++ V + T DDL F + G V + I++ D+ T
Sbjct: 4 GSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKET 61
Query: 54 GDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGP 96
G +G A V Y+ A+ AV+ DG+ G ++ V A+ P
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKP 104
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 44/76 (57%), Gaps = 7/76 (9%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDI-FIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
+LL N++F T D+L +F+ ++I + +D G S+G A++ +K +A+K ++
Sbjct: 101 TLLAKNLSFNITEDELKEVFED---ALEIRLVSQD---GKSKGIAYIEFKSEADAEKNLE 154
Query: 76 RLDGRVVDGREITVQF 91
G +DGR +++ +
Sbjct: 155 EKQGAEIDGRSVSLYY 170
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 35/53 (66%), Gaps = 2/53 (3%)
Query: 50 DRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGPNAERIK 102
D RTG +R F +V ++ A++ +KA++ L G V G EI ++ K G ++++++
Sbjct: 47 DVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLEKPK-GRDSKKVR 97
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 43/88 (48%), Gaps = 15/88 (17%)
Query: 2 SHFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAF 61
SH G SG + + ++++TT + L F ++G+V + + RD T SRGF F
Sbjct: 19 SHMGSSG-------CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGF 71
Query: 62 VRYKYADEA------QKAVDRLDGRVVD 83
V + D+A ++ LD + +D
Sbjct: 72 V--TFMDQAGVDKVLAQSRHELDSKTID 97
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 32/58 (55%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
+ V ++ TT +D+ F+++GKV D + D+ T RGF FV ++ D +K +
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 32/106 (30%), Positives = 51/106 (48%), Gaps = 9/106 (8%)
Query: 2 SHFGRSGPPDITDTYS--LLVLNIT-FRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRG 58
SH GR P + + LLV N+ R T LF LF YG V + I +++
Sbjct: 19 SHMGRIAIPGLAGAGNSVLLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN---- 74
Query: 59 FAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGPNAERIKEG 104
A V+ ++AQ A+ L+G + G+ I + +K+ N + +EG
Sbjct: 75 -ALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKH-QNVQLPREG 118
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/83 (30%), Positives = 42/83 (50%), Gaps = 6/83 (7%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGK--VVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAV 74
++++ NI T D + Y V +I + +D++T +RGFAFV+ A +A + +
Sbjct: 11 TIILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLL 70
Query: 75 DRLDG----RVVDGREITVQFAK 93
L +DG+ I V FAK
Sbjct: 71 QILQSLHPPLKIDGKTIGVDFAK 93
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G SG + L V N+ T + L F ++GK+ + +D +AF+ +
Sbjct: 1 GSSGSSGMAKVKVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKD--------YAFIHF 52
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQFAK 93
D A KA++ ++G+ ++G I + FAK
Sbjct: 53 DERDGAVKAMEEMNGKDLEGENIEIVFAK 81
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 31/97 (31%), Positives = 49/97 (50%), Gaps = 13/97 (13%)
Query: 4 FGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
+G++ P T L V + T+ L FD++G + I D GDS FA+++
Sbjct: 11 YGKANP-----TTRLWVGGLGPNTSLAALAREFDRFGSIRTI----DHVKGDS--FAYIQ 59
Query: 64 YKYADEAQKAVDRLDGRVVDG--REITVQFAKYGPNA 98
Y+ D AQ A ++ G + G R + V FAK GP++
Sbjct: 60 YESLDAAQAACAKMRGFPLGGPDRRLRVDFAKSGPSS 96
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 33/78 (42%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T L +G + F+ RTG S+G+ F Y D A +A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 78 DGRVVDGREITVQFAKYG 95
G+ + R + V + G
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 54 GDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGP 96
G +GFA + Y+ A+ A++A + DG + G + V F GP
Sbjct: 223 GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP 265
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 33/78 (42%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T L +G + F+ RTG S+G+ F Y D A +A L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 78 DGRVVDGREITVQFAKYG 95
G+ + R + V + G
Sbjct: 158 LGKPLGPRTLYVHWTDAG 175
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 54 GDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGP 96
G +GFA + Y+ A+ A++A + DG + G + V F GP
Sbjct: 223 GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP 265
>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 = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 33/78 (42%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V N+ T L +G + F+ RTG S+G+ F Y D A +A L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 78 DGRVVDGREITVQFAKYG 95
G+ + R + V + G
Sbjct: 156 LGKPLGPRTLYVHWTDAG 173
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 54 GDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGP 96
G +GFA + Y+ A+ A++A + DG + G + V F GP
Sbjct: 221 GQLKGFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAPGP 263
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 40/75 (53%), Gaps = 1/75 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+L V N++F TT + ++ LF K G + I + D+ + GF FV Y +A+ A+
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKT-ACGFCFVEYYSRADAENAMRY 78
Query: 77 LDGRVVDGREITVQF 91
++G +D R I +
Sbjct: 79 INGTRLDDRIIRTDW 93
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L + +F ++G+++DI + R + RG AFV +K
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFK 60
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 88
>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 = 0.009, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 33/73 (45%), Gaps = 6/73 (8%)
Query: 27 TTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGRE 86
TT DL L YGK+V D+ T +G+ FV + AQKAV L V
Sbjct: 17 TTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVTALKASGVQA-- 74
Query: 87 ITVQFAKY-GPNA 98
Q AK GP++
Sbjct: 75 ---QMAKQSGPSS 84
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 5/82 (6%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
++ V N+ R + L+ LF + G + + I +DR G + F FV +K+ + A+
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 77 LDGRVVDGREITVQFAKYGPNA 98
L+G + GR I V GP++
Sbjct: 77 LNGIRLYGRPINVS----GPSS 94
>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 = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D S+ V N+ + TA++L F G V + I D+ +G +GFA++ + + + +
Sbjct: 4 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 63
Query: 74 VDRLDGRVVDGREITV 89
+ LD + GR+I V
Sbjct: 64 L-ALDESLFRGRQIKV 78
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
28
Length = 111
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/90 (25%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 9 PPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYAD 68
P D+T+ ++ + N++F + + L + ++G + + + T S+G AF ++ +
Sbjct: 9 PSDVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQE 68
Query: 69 EAQK--AVDRLD----GRVVDGREITVQFA 92
AQK A L+ G +DGR++ V A
Sbjct: 69 AAQKCLAAASLEAEGGGLKLDGRQLKVDLA 98
>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 = 28/86 (32%), Positives = 43/86 (50%), Gaps = 8/86 (9%)
Query: 10 PDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTG--DSRGFAFVRY--- 64
PD+ D + V + + DL LF++YG V +I + RDR S+G FV +
Sbjct: 11 PDL-DAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR 69
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQ 90
K A EAQ A+ + +V+ G +Q
Sbjct: 70 KAALEAQNALHNM--KVLPGMHHPIQ 93
>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 = 36.6 bits (83), Expect = 0.015, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 1/76 (1%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D S+ V N+ + TA++L F G V + I D+ +G +GFA++ + + + +
Sbjct: 5 DARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTS 64
Query: 74 VDRLDGRVVDGREITV 89
+ LD + GR+I V
Sbjct: 65 L-ALDESLFRGRQIKV 79
>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 = 36.6 bits (83), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 45/81 (55%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
SL V ++ T L+ F G ++ I + RD T S G+A+V ++ +A++A+D
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 77 LDGRVVDGREITVQFAKYGPN 97
++ V+ G+ + + +++ P+
Sbjct: 77 MNFDVIKGKPVRIMWSQRDPS 97
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 45/87 (51%), Gaps = 7/87 (8%)
Query: 11 DITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKY 66
DI +++ + N+ + ++L + LF ++G VVDI + T RG AFV +K
Sbjct: 2 DIRPNHTIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALK---TMKMRGQAFVIFKE 58
Query: 67 ADEAQKAVDRLDGRVVDGREITVQFAK 93
+ A+ +L G G+ + +Q+AK
Sbjct: 59 LGSSTNALRQLQGFPFYGKPMRIQYAK 85
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
LLV N+ F + D+ LF ++G + + DR +G S G A V ++ +A KA+ +
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQY 89
Query: 78 DGRVVDGREITVQ 90
+G +DGR + +Q
Sbjct: 90 NGVPLDGRPMNIQ 102
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 36.6 bits (83), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 39/75 (52%), Gaps = 8/75 (10%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V NI+ T +L F++YG V++ I +D +AFV + A++A +A+ L
Sbjct: 13 LHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAIRGL 64
Query: 78 DGRVVDGREITVQFA 92
D G+ + VQ +
Sbjct: 65 DNTEFQGKRMHVQLS 79
>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 = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 45/81 (55%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
SL V ++ T L+ F G ++ I + RD T S G+A+V ++ +A++A+D
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 77 LDGRVVDGREITVQFAKYGPN 97
++ V+ G+ + + +++ P+
Sbjct: 72 MNFDVIKGKPVRIMWSQRDPS 92
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 13 TDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTG--DSRGFAFVRY---KYA 67
+D + V + + DL LF++YG V +I + RDR S+G FV + K A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 68 DEAQKAVDRL 77
EAQ A+ +
Sbjct: 61 LEAQNALHNM 70
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 36.2 bits (82), Expect = 0.020, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 9/74 (12%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREI 87
TA++L F +YG+VVD+FIP+ R FAFV +AD+ K L G + + I
Sbjct: 24 TAEELQQFFCQYGEVVDVFIPK-----PFRAFAFV--TFADD--KVAQSLCGEDLIIKGI 74
Query: 88 TVQFAKYGPNAERI 101
+V + P ++
Sbjct: 75 SVHISNAEPKHNKL 88
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In
Imidazole And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With
C75u Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 60
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 88
>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 = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 17/64 (26%), Positives = 35/64 (54%)
Query: 22 NITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRV 81
+I + T + + L G V+++ + D +TG S+G+AF+ ++ + + AV L+G
Sbjct: 11 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 70
Query: 82 VDGR 85
+ R
Sbjct: 71 LGSR 74
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 59
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX
THAT Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V.
Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase
Ribozyme-Substrate Preligation Complex, C47u Mutant,
Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 60
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 61 EVSSATNALRSMQGFPFYDKPMRIQYAK 88
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 22 NITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRV 81
+I + T + + L G V+++ + D +TG S+G+AF+ ++ + + AV L+G
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 82 VDGREITVQFAK 93
+ R + ++
Sbjct: 69 LGSRFLKCGYSS 80
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 45/88 (51%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L + +F ++G+++DI + R + RG AFV +K
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKM---RGQAFVIFK 59
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
Length = 97
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 59
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 35.8 bits (81), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 59
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 60 EVSSATNALRSMQGFPFYDKPMRIQYAK 87
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFK 57
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ + G + + +Q+AK
Sbjct: 58 EVSSATNALRSMQGFPFYDKPMRIQYAK 85
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 35.8 bits (81), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 1/87 (1%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G G + LLV N+ F + D+ LF ++G + + DR +G S G A V +
Sbjct: 25 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 83
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQF 91
+ +A KA+ + G +DGR + +Q
Sbjct: 84 ERRADALKAMKQYKGVPLDGRPMDIQL 110
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 35.4 bits (80), Expect = 0.030, Method: Composition-based stats.
Identities = 21/74 (28%), Positives = 37/74 (50%), Gaps = 12/74 (16%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR- 76
+ + ++++TT + L F ++G+V + + RD T SRGF FV + Q VD+
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM----DQAGVDKV 58
Query: 77 -------LDGRVVD 83
LD + +D
Sbjct: 59 LAQSRHELDSKTID 72
>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 = 35.4 bits (80), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 38/72 (52%)
Query: 22 NITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRV 81
+I + T + + L G V+++ + D +TG S+G+AF+ ++ + + AV L+G
Sbjct: 10 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 69
Query: 82 VDGREITVQFAK 93
+ R + ++
Sbjct: 70 LGSRFLKCGYSS 81
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 1/87 (1%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G G + LLV N+ F + D+ LF ++G + + DR +G S G A V +
Sbjct: 25 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 83
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQF 91
+ +A KA+ + G +DGR + +Q
Sbjct: 84 ERRADALKAMKQYKGVPLDGRPMDIQL 110
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 35.4 bits (80), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 43/87 (49%), Gaps = 1/87 (1%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G G + LLV N+ F + D+ LF ++G + + DR +G S G A V +
Sbjct: 78 GCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDR-SGRSLGTADVHF 136
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQF 91
+ +A KA+ + G +DGR + +Q
Sbjct: 137 ERRADALKAMKQYKGVPLDGRPMDIQL 163
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 8/63 (12%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
D+ +F KYG+V + +G+AFV+Y A+ AV +GRV+ G+ + +
Sbjct: 43 SDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVLGENGRVLAGQTLDI 94
Query: 90 QFA 92
A
Sbjct: 95 NMA 97
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 44/88 (50%), Gaps = 7/88 (7%)
Query: 18 LLVLNIT-FRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
LLV N+ R T LF LF YG V + I +++ A V+ ++AQ A+
Sbjct: 6 LLVSNLNPERVTPQSLFILFGVYGDVQRVKILFNKKEN-----ALVQMADGNQAQLAMSH 60
Query: 77 LDGRVVDGREITVQFAKYGPNAERIKEG 104
L+G + G+ I + +K+ N + +EG
Sbjct: 61 LNGHKLHGKPIRITLSKH-QNVQLPREG 87
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 40/88 (45%), Gaps = 1/88 (1%)
Query: 10 PDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADE 69
P+ D ++ + + R DL F GKV D+ I DR + S+G A+V +
Sbjct: 20 PEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQS 79
Query: 70 AQKAVDRLDGRVVDGREITVQFAKYGPN 97
A+ L G+ + G I VQ ++ N
Sbjct: 80 VPLAIG-LTGQRLLGVPIIVQASQAEKN 106
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 40/85 (47%), Gaps = 5/85 (5%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+ V N+ +L F YG + ++I R+ GFAFV ++ +A+ AV
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 77 LDGRVVDGREITVQFAKYGPNAERI 101
LDG+V+ G + V+ + P R
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRSRF 81
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.0 bits (79), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
Query: 14 DTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKA 73
D +L + N+ +L + +G+V+ I RD +G SRG F R + ++ +
Sbjct: 24 DPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAV 82
Query: 74 VDRLDGRVV 82
+ +G+ +
Sbjct: 83 IGHFNGKFI 91
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 34.7 bits (78), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
LLV N+ F + D+ LF ++G + + DR +G S G A V ++ +A KA +
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQY 90
Query: 78 DGRVVDGREITVQ 90
+G +DGR +Q
Sbjct: 91 NGVPLDGRPXNIQ 103
>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 = 34.3 bits (77), Expect = 0.067, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 7/83 (8%)
Query: 13 TDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTG--DSRGFAFVRY---KYA 67
+D + V + + DL LF++YG V +I + RDR S+G FV + K A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 68 DEAQKAVDRLDGRVVDGREITVQ 90
EAQ A+ + +V+ G +Q
Sbjct: 61 LEAQNALHNM--KVLPGMHHPIQ 81
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.3 bits (77), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 44/95 (46%), Gaps = 14/95 (14%)
Query: 5 GRSGPPDITDTYS----LLVLNITFRTTADDLFPLFD--KYGKVVDIFIPRDRRTGDSRG 58
G SG DT S L V N+ T+ + + F+ K G V R R
Sbjct: 1 GSSGSSGDEDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAV--------ERVKKIRD 52
Query: 59 FAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAK 93
+AFV + ++A +A+ L+G+V+DG I V AK
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAK 87
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 34.3 bits (77), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 23/92 (25%), Positives = 45/92 (48%), Gaps = 5/92 (5%)
Query: 7 SGPPDITDTYSLLVLNITFRTTADDLFPLFDKYG--KVVDIFIPRDRRTGDSRGFAFVRY 64
S P ++++ N+ +T D + Y ++ + +D++T +RGFAF++
Sbjct: 15 SEPSSENANDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQL 74
Query: 65 KYADEAQ--KAVDRLD-GRVVDGREITVQFAK 93
+ AQ + + L +DG+ I V+FAK
Sbjct: 75 STIEAAQLLQILQALHPPLTIDGKTINVEFAK 106
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 33.9 bits (76), Expect = 0.086, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 28 TADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQ 71
T D+L F +YG V+D+FIP+ R FAFV + AQ
Sbjct: 18 TEDELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIAQ 56
>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 = 33.9 bits (76), Expect = 0.096, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 36 FDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
F +G+V I +P D +T RGF F+ +K + +K +++
Sbjct: 22 FGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 33.9 bits (76), Expect = 0.096, Method: Composition-based stats.
Identities = 13/41 (31%), Positives = 24/41 (58%)
Query: 36 FDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
F +G+V I +P D +T RGF F+ +K + +K +++
Sbjct: 20 FGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 25/40 (62%)
Query: 54 GDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAK 93
G S+GF FV + +EA KAV ++GR+V + + V A+
Sbjct: 52 GRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
>pdb|2CQ2|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Loc91801
Length = 114
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 46/80 (57%), Gaps = 11/80 (13%)
Query: 15 TYSLLVLN--ITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T SL+V N + + + L P+ +K G V + +P ++ ++F RY+ +E+++
Sbjct: 25 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNKP------YSFARYRTTEESKR 78
Query: 73 AVDRLDGR-VVD--GREITV 89
A L+G+ VVD G++IT+
Sbjct: 79 AYVTLNGKEVVDDLGQKITL 98
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 15 TYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEA 70
+++ + N+ + D+L +F ++G+++DI + R + RG AFV +K A
Sbjct: 4 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSA 60
Query: 71 QKAVDRLDGRVVDGREITVQFAK 93
A+ + G + + +Q+AK
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYAK 83
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 29/88 (32%), Positives = 44/88 (50%), Gaps = 4/88 (4%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
GP D + V N+ D+ +F KYG + DI + ++RR G FAFV ++
Sbjct: 16 GPAGNNDC-RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDP 71
Query: 68 DEAQKAVDRLDGRVVDGREITVQFAKYG 95
+A+ AV DG DG + V+F + G
Sbjct: 72 RDAEDAVYGRDGYDYDGYRLRVEFPRSG 99
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms
Ribozyme Bound To Glc6p
Length = 90
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 15 TYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEA 70
+++ + N+ + D+L +F ++G+++DI + R + RG AFV +K A
Sbjct: 3 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSA 59
Query: 71 QKAVDRLDGRVVDGREITVQFAK 93
A+ + G + + +Q+AK
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYAK 82
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To
Its Catalytic Cofactor
Length = 94
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 15 TYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEA 70
+++ + N+ + D+L +F ++G+++DI + R + RG AFV +K A
Sbjct: 5 NHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKM---RGQAFVIFKEVSSA 61
Query: 71 QKAVDRLDGRVVDGREITVQFAK 93
A+ + G + + +Q+AK
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYAK 84
>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 = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 44/81 (54%), Gaps = 5/81 (6%)
Query: 28 TADDLFPLFDKYG-KVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRV-VDGR 85
T DD+ +G + ++ + R++ +G SRGFAFV + + +A + ++ + + G+
Sbjct: 14 TEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWMEANQHSLNILGQ 73
Query: 86 EITVQFAKYGPNAERIKEGLL 106
++++ ++ P +I E L
Sbjct: 74 KVSMHYSDPKP---KINEDWL 91
>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 = 0.12, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 40/83 (48%), Gaps = 7/83 (8%)
Query: 13 TDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTG--DSRGFAFVRY---KYA 67
+D V + + DL LF++YG V +I + RDR S+G FV + K A
Sbjct: 1 SDAIKXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 68 DEAQKAVDRLDGRVVDGREITVQ 90
EAQ A+ + +V+ G +Q
Sbjct: 61 LEAQNALH--NXKVLPGXHHPIQ 81
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 40/83 (48%), Gaps = 2/83 (2%)
Query: 8 GPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYA 67
G + + V N+ F T L F++ G V+ I + G S+G V+++
Sbjct: 1 GSSGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME--NGKSKGCGVVKFESP 58
Query: 68 DEAQKAVDRLDGRVVDGREITVQ 90
+ A++A ++G + GREI V+
Sbjct: 59 EVAERACRMMNGMKLSGREIDVR 81
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKX---RGQAFVIFK 57
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ G + +Q+AK
Sbjct: 58 EVSSATNALRSXQGFPFYDKPXRIQYAK 85
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKX---RGQAFVIFK 59
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ G + +Q+AK
Sbjct: 60 EVSSATNALRSXQGFPFYDKPXRIQYAK 87
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 21/88 (23%), Positives = 42/88 (47%), Gaps = 7/88 (7%)
Query: 10 PDITDTYSLLVLNITFRTTADDL----FPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYK 65
P+ +++ + N+ + D+L +F ++G+++DI + R + RG AFV +K
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKX---RGQAFVIFK 60
Query: 66 YADEAQKAVDRLDGRVVDGREITVQFAK 93
A A+ G + +Q+AK
Sbjct: 61 EVSSATNALRSXQGFPFYDKPXRIQYAK 88
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 35 LFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVD 83
+F K+GK+ + F P + G ++G+ F+ Y A AV DG +D
Sbjct: 27 IFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 22/43 (51%)
Query: 50 DRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFA 92
DR TG +G A V + A+ A+D DG+ G I V FA
Sbjct: 56 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 98
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 39/76 (51%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L + N++ R T DL LF ++ + I TG RG AF+ + + A +A+ +
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALHLV 87
Query: 78 DGRVVDGREITVQFAK 93
+G + G+ + ++F K
Sbjct: 88 NGYKLYGKILVIEFGK 103
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 9/72 (12%)
Query: 36 FDKYGKVVDIFIPRDRRTGDSRG---FAFVRYKYADEAQKAVDRLDGRVVDGREI----- 87
F K+GK+ + I S+G A+V Y +++A +A+ ++ VVDGR +
Sbjct: 39 FGKFGKIHKVVINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASLG 98
Query: 88 TVQFAKY-GPNA 98
T ++ Y GP++
Sbjct: 99 TTKYCSYSGPSS 110
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 1/62 (1%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + + + +D+ LF +G + + + R G S+G AFV++ EAQ A+ L
Sbjct: 18 LFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGP-DGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 78 DG 79
G
Sbjct: 77 HG 78
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 32.3 bits (72), Expect = 0.28, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 33/66 (50%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
D + L +G + + +D TG S+G+AF Y + +A+ L+G + +++ V
Sbjct: 16 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 75
Query: 90 QFAKYG 95
Q A G
Sbjct: 76 QRASVG 81
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 32/62 (51%), Gaps = 6/62 (9%)
Query: 36 FDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYG 95
F +G++++I R +G++FVR+ + A A+ ++G ++G + + K
Sbjct: 46 FSPFGQIMEI------RVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWGKES 99
Query: 96 PN 97
P+
Sbjct: 100 PD 101
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 26/93 (27%), Positives = 44/93 (47%), Gaps = 10/93 (10%)
Query: 10 PDITDTYSLL--------VLNITFRTTADDLFPLFDKYG--KVVDIFIPRDRRTGDSRGF 59
P I TYS L V + ++ TT L + G VV++ +R G S+G+
Sbjct: 42 PAILYTYSGLRNRRAAVYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGY 101
Query: 60 AFVRYKYADEAQKAVDRLDGRVVDGREITVQFA 92
A V + K ++ L G+V++G ++ V+ A
Sbjct: 102 AEVVVASENSVHKLLELLPGKVLNGEKVDVRPA 134
>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 = 0.36, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 51/97 (52%), Gaps = 19/97 (19%)
Query: 15 TYSLLVLN--ITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T SL+V N + + + L P+ +K G V + +P ++ ++F RY+ +E+++
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLMPPNK------PYSFARYRTTEESKR 71
Query: 73 AVDRLDGR-VVD--GREIT--------VQFAKYGPNA 98
A L+G+ VVD G++IT VQ+ + P A
Sbjct: 72 AYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQA 108
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 32.0 bits (71), Expect = 0.42, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
++ V I R ++ F +YG V ++ I DR TG S+G+ FV + + QK V+
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 69
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 22/43 (51%)
Query: 50 DRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFA 92
DR TG +G A V + A+ A+D DG+ G I V FA
Sbjct: 50 DRETGKLKGEATVSFDDPPSAKAAIDWFDGKEFSGNPIKVSFA 92
>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 = 31.6 bits (70), Expect = 0.46, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
++ V I R ++ F +YG V ++ I DR TG S+G+ FV + + QK V+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
D + L +G + + +D TG S+G+AF Y + +A+ L+G + +++ V
Sbjct: 129 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 188
Query: 90 QFAKYG 95
Q A G
Sbjct: 189 QRASVG 194
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 31.6 bits (70), Expect = 0.50, Method: Composition-based stats.
Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 4/83 (4%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
+ V N+ F T L F++ G V ++ G S+G V+++ + A++A +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRMM 65
Query: 78 DGRVVDGREITVQFAK--YGPNA 98
+G + GREI V+ + GP++
Sbjct: 66 NGMKLSGREIDVRIDRNASGPSS 88
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 31.6 bits (70), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%), Gaps = 5/62 (8%)
Query: 42 VVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDG----REITVQFAKY-GP 96
V+ + I R+R TG G+ FV + A+K + +++G+ + G + + +A Y GP
Sbjct: 37 VMSVKIIRNRLTGIPAGYCFVEFADLATAEKCLHKINGKPLPGATPAKRFKLNYATYSGP 96
Query: 97 NA 98
++
Sbjct: 97 SS 98
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 31.2 bits (69), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 32/68 (47%), Gaps = 7/68 (10%)
Query: 32 LFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGRE----- 86
+ +F K+GK+ + F P + G ++G+ F+ Y A AV DG +D +
Sbjct: 38 IHKIFSKFGKITNDFYPEE--DGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVN 95
Query: 87 ITVQFAKY 94
+ F KY
Sbjct: 96 LFTDFDKY 103
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 31.2 bits (69), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 25/88 (28%), Positives = 47/88 (53%), Gaps = 8/88 (9%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRL 77
L V + + T +D+ +F+ +G + + + R G S+G AFV+++ EAQ A++ L
Sbjct: 15 LFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGP-DGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 78 -DGRVVDG--REITVQFA----KYGPNA 98
R + G + V+FA + GP++
Sbjct: 74 HSSRTLPGASSSLVVKFADTEKESGPSS 101
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 42/92 (45%), Gaps = 9/92 (9%)
Query: 2 SHFGRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAF 61
SH ++++T L V +L +F +G + ++ I GFAF
Sbjct: 19 SHMHHRQEGELSNT-RLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAF 69
Query: 62 VRYKYADEAQKAVDRLDGRVVDGREITVQFAK 93
V ++ A+ A KA++ + G+ + + V ++K
Sbjct: 70 VEFEEAESAAKAIEEVHGKSFANQPLEVVYSK 101
>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 = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 16/35 (45%), Positives = 19/35 (54%)
Query: 18 LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRR 52
L LN+ A D F L+ K GK DI +PR RR
Sbjct: 105 LRQLNLKNYQAAADAFLLWKKAGKDPDILLPRRRR 139
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 30.4 bits (67), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 10/63 (15%)
Query: 36 FDKYGKVVDIFI--PRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAK 93
F +G ++D+ + PR+ AFV Y+ + A +AV L+G V+ ++ V A+
Sbjct: 34 FSPFGNIIDLSMDPPRN--------CAFVTYEKMESADQAVAELNGTQVESVQLKVNIAR 85
Query: 94 YGP 96
P
Sbjct: 86 KQP 88
>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 = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 50/97 (51%), Gaps = 19/97 (19%)
Query: 15 TYSLLVLN--ITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQK 72
T SL+V N + + + L P+ +K G V + P ++ ++F RY+ +E+++
Sbjct: 18 TQSLVVANGGLGNGVSRNQLLPVLEKCGLVDALLXPPNK------PYSFARYRTTEESKR 71
Query: 73 AVDRLDGR-VVD--GREIT--------VQFAKYGPNA 98
A L+G+ VVD G++IT VQ+ + P A
Sbjct: 72 AYVTLNGKEVVDDLGQKITLYLNFVEKVQWKELRPQA 108
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.4 bits (67), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+ V N+ +L F YG + +++ R+ GFAFV ++ +A AV
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRE 129
Query: 77 LDGRVVDGREITVQFAK 93
LDGR + G + V+ +
Sbjct: 130 LDGRTLCGCRVRVELSN 146
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
++ V I R ++ F +YG V ++ I DR TG S+G+ FV + + QK V+
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/89 (24%), Positives = 40/89 (44%), Gaps = 11/89 (12%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G SG + L + N+ T ++ LF++YGKV++ I ++ + FV
Sbjct: 1 GSSGSSGMVK---LFIGNLPREATEQEIRSLFEQYGKVLECDIIKN--------YGFVHI 49
Query: 65 KYADEAQKAVDRLDGRVVDGREITVQFAK 93
+ A+ A+ L + G I V+ +K
Sbjct: 50 EDKTAAEDAIRNLHHYKLHGVNINVEASK 78
>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 = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 30/61 (49%), Gaps = 6/61 (9%)
Query: 36 FDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYG 95
F +G ++D+ + R AFV Y+ + A +AV L+G V+ ++ V A+
Sbjct: 58 FSPFGNIIDLSM------DPPRNCAFVTYEKMESADQAVAELNGTQVESVQLKVNIARKQ 111
Query: 96 P 96
P
Sbjct: 112 P 112
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.0 bits (66), Expect = 1.3, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 2/63 (3%)
Query: 33 FPLFDKYGKVVDIFIPRD--RRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQ 90
FPL + ++ +IF P + GFAFV ++ A+ A KA++ + G+ + + V
Sbjct: 12 FPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFANQPLEVV 71
Query: 91 FAK 93
++K
Sbjct: 72 YSK 74
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 10/89 (11%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRY 64
G SG + Y + N++ TADDL LF D +P + G+AFV Y
Sbjct: 1 GSSGSSGMNKLY---IGNLSPAVTADDLRQLFG------DRKLPLAGQVLLKSGYAFVDY 51
Query: 65 KYADEAQKAVDRLDGRV-VDGREITVQFA 92
+ A +A++ L G+V + G+ + V ++
Sbjct: 52 PDQNWAIRAIETLSGKVELHGKIMEVDYS 80
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 30.0 bits (66), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 27/41 (65%), Gaps = 1/41 (2%)
Query: 50 DRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITVQ 90
D RTG +R F +V ++ A++ +KA++ L G V G EI ++
Sbjct: 51 DVRTGTNRKFGYVDFESAEDLEKALE-LTGLKVFGNEIKLE 90
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
DD+ +K+G V+ I++ ++ ++G +V+ A AV+ L GR G+ IT
Sbjct: 32 DDVIEECNKHGGVIHIYVDKN----SAQGNVYVKCPSIAAAIAAVNALHGRWFAGKXITA 87
Query: 90 QF 91
+
Sbjct: 88 AY 89
>pdb|3F7M|A Chain A, Crystal Structure Of Apo Cuticle-Degrading Protease
(Ver112) From Verticillium Psalliotae
Length = 279
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 11/22 (50%), Positives = 15/22 (68%)
Query: 27 TTADDLFPLFDKYGKVVDIFIP 48
T ++D+ F YG+VVDIF P
Sbjct: 184 TDSNDVRSTFSNYGRVVDIFAP 205
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 29.6 bits (65), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 58 GFAFVRYKYADEAQKAVDRLDGRVVDGREITVQ 90
G A V ++ +EA + LDGR GR+IT Q
Sbjct: 65 GVASVSFRDPEEADYCIQTLDGRWFGGRQITAQ 97
>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 = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
D + L +G + + +D TG S+G+AF Y + +A+ L+G + +++ V
Sbjct: 111 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 170
Query: 90 QFA 92
Q A
Sbjct: 171 QRA 173
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 8/89 (8%)
Query: 16 YSLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVD 75
Y+ V N+ F T D+ +F K + + + RD+ T +GF +V + D ++A+
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIF-KDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL- 73
Query: 76 RLDGRVVDGREITVQFA------KYGPNA 98
DG ++ R + V A K GP++
Sbjct: 74 TYDGALLGDRSLRVDIAEGRKQDKSGPSS 102
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 36/77 (46%), Gaps = 5/77 (6%)
Query: 17 SLLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDR 76
+ V N+ +L F YG + +++ R+ GFAFV ++ +A AV
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVRD 129
Query: 77 LDGRVVDGREITVQFAK 93
LDGR + G + V+ +
Sbjct: 130 LDGRTLCGCRVRVELSN 146
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
D + L +G + + +D TG S+G+AF Y + +A+ L+G + +++ V
Sbjct: 109 DQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLGDKKLLV 168
Query: 90 QFA 92
Q A
Sbjct: 169 QRA 171
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From
Mus Musculus
Length = 113
Score = 29.3 bits (64), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 30 DDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVRYKYADEAQKAVDRLDGRVVDGREITV 89
DD+ +K+G V+ I++ ++ ++G +V+ A AV+ L GR G+ IT
Sbjct: 31 DDVIEECNKHGGVIHIYVDKN----SAQGNVYVKCPSIAAAIAAVNALHGRWFAGKMITA 86
Query: 90 QF 91
+
Sbjct: 87 AY 88
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 5 GRSGPPDITDTYS-LLVLNITFRTTADDLFPLFDKYGKVVDIFIPRDRRTGDSRGFAFVR 63
G SG P++ L V N+ T + L F ++GK+ + +D +AFV
Sbjct: 4 GSSGDPEVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKD--------YAFVH 55
Query: 64 YKYADEAQKAVDRLDGR 80
++ A KA+D ++G+
Sbjct: 56 FEDRGAAVKAMDEMNGK 72
>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 = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 21 LNITFRTTADDLFPLFDKYGKVVDIF--IPRDR 51
L FR +D ++ +F +Y K+VD + IP DR
Sbjct: 42 LYYHFRNKSDIIYEIFQEYEKLVDYYLDIPEDR 74
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 27.7 bits (60), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 61 FVRYKYADEAQKAVDRLDGRVVDGREITVQ 90
FV + A E KA+ L+GR GR++ +
Sbjct: 179 FVEFSIASETHKAIQALNGRWFAGRKVVAE 208
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 27.3 bits (59), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 32/104 (30%), Positives = 47/104 (45%), Gaps = 18/104 (17%)
Query: 5 GRSGPPDITDTYSLLVLNITFRTTADDLFPLFDKY------GKVVDIFIPRDRRTGDSRG 58
G SGP YSL V ++T L+ F K GKVV +TG S+G
Sbjct: 4 GSSGP-----EYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVL------DQTGVSKG 52
Query: 59 FAFVRYKYADEAQKAVDRLDGRVVDGREITVQFAKYGPNAERIK 102
+ FV++ E ++A+ G V G + V+ + P A R+K
Sbjct: 53 YGFVKFTDELEQKRALTECQGAVGLGSK-PVRLSVAIPKASRVK 95
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
0.323 0.142 0.408
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,140,932
Number of Sequences: 62578
Number of extensions: 266908
Number of successful extensions: 861
Number of sequences better than 100.0: 202
Number of HSP's better than 100.0 without gapping: 148
Number of HSP's successfully gapped in prelim test: 54
Number of HSP's that attempted gapping in prelim test: 659
Number of HSP's gapped (non-prelim): 229
length of query: 270
length of database: 14,973,337
effective HSP length: 97
effective length of query: 173
effective length of database: 8,903,271
effective search space: 1540265883
effective search space used: 1540265883
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)