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= 022981
(289 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 92.8 bits (229), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 46/71 (64%), Positives = 55/71 (77%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
IYVGNLP DIR ++ED+FYKYG I DI+LK P + FVEFE+ RDAEDA+ GRDGY
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGY 84
Query: 69 NFDGCRLRVEL 79
++DG RLRVE
Sbjct: 85 DYDGYRLRVEF 95
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 83.6 bits (205), Expect = 1e-16, Method: Compositional matrix adjust.
Identities = 42/86 (48%), Positives = 55/86 (63%), Gaps = 22/86 (25%)
Query: 123 SEYRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGT 182
S++RV+V GLP S SWQDLKDHMR+AGDVC+A+V +D
Sbjct: 14 SDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDG---------------------- 51
Query: 183 YGVVDYTNPEDMKYAIRKLDDTEFRN 208
G+V+Y EDM+YA+RKLDDT+FR+
Sbjct: 52 MGMVEYLRKEDMEYALRKLDDTKFRS 77
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 45/86 (52%), Positives = 55/86 (63%), Gaps = 22/86 (25%)
Query: 123 SEYRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGT 182
SE RV+V GLP S SWQDLKDHMR+AGDVC+A+V RD GT
Sbjct: 14 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---------------------GT 52
Query: 183 YGVVDYTNPEDMKYAIRKLDDTEFRN 208
GVV++ EDM YA+RKLD+T+FR+
Sbjct: 53 -GVVEFVRKEDMTYAVRKLDNTKFRS 77
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 82.4 bits (202), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 45/86 (52%), Positives = 55/86 (63%), Gaps = 22/86 (25%)
Query: 123 SEYRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGT 182
SE RV+V GLP S SWQDLKDHMR+AGDVC+A+V RD GT
Sbjct: 15 SENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---------------------GT 53
Query: 183 YGVVDYTNPEDMKYAIRKLDDTEFRN 208
GVV++ EDM YA+RKLD+T+FR+
Sbjct: 54 -GVVEFVRKEDMTYAVRKLDNTKFRS 78
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 80.9 bits (198), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 44/85 (51%), Positives = 54/85 (63%), Gaps = 22/85 (25%)
Query: 124 EYRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGTY 183
E RV+V GLP S SWQDLKDHMR+AGDVC+A+V RD GT
Sbjct: 15 ENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---------------------GT- 52
Query: 184 GVVDYTNPEDMKYAIRKLDDTEFRN 208
GVV++ EDM YA+RKLD+T+FR+
Sbjct: 53 GVVEFVRKEDMTYAVRKLDNTKFRS 77
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 62.4 bits (150), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 32/73 (43%), Positives = 46/73 (63%), Gaps = 2/73 (2%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
+YVGNL ++ + E+E F YG + + + PP + FVEFE+ RDA DA+R DG
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRDLDGR 133
Query: 69 NFDGCRLRVELAH 81
GCR+RVEL++
Sbjct: 134 TLCGCRVRVELSN 146
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 62.0 bits (149), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 32/73 (43%), Positives = 46/73 (63%), Gaps = 2/73 (2%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
+YVGNL ++ + E+E F YG + + + PP + FVEFE+ RDA DA+R DG
Sbjct: 76 VYVGNLGNNGNKTELERAFGYYGPLRSV--WVARNPPGFAFVEFEDPRDAADAVRELDGR 133
Query: 69 NFDGCRLRVELAH 81
GCR+RVEL++
Sbjct: 134 TLCGCRVRVELSN 146
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 60.5 bits (145), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 34/72 (47%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
+YVGNL + + E+E F YG + + I PP + FVEFE+ RDAEDA+RG DG
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVW--IARNPPGFAFVEFEDPRDAEDAVRGLDGK 60
Query: 69 NFDGCRLRVELA 80
G R+RVEL+
Sbjct: 61 VICGSRVRVELS 72
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/75 (36%), Positives = 44/75 (58%), Gaps = 3/75 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGR 65
++VG L D E +E +F KYG+I ++ + + R + FV FEN DA+DA+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 66 DGYNFDGCRLRVELA 80
+G + DG ++RV+ A
Sbjct: 75 NGKSVDGRQIRVDQA 89
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 50.4 bits (119), Expect = 1e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 38/70 (54%), Gaps = 5/70 (7%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
+++GNLP + E E+ LF +YG++L+ ++ Y FV E+ AEDAIR Y
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDII-----KNYGFVHIEDKTAAEDAIRNLHHY 65
Query: 69 NFDGCRLRVE 78
G + VE
Sbjct: 66 KLHGVNINVE 75
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPR---PPCYCFVEFENARDAEDAIRG 64
T+ V NL + +F KYGR+ D+ + P P + FV F + RDA+DA
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAA 74
Query: 65 RDGYNFDGCRLRVELA 80
DG DG LRV++A
Sbjct: 75 MDGAELDGRELRVQVA 90
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 45/80 (56%), Gaps = 3/80 (3%)
Query: 4 RFSRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAED 60
R R+++VGN+P + E +++D+F + G ++ L + +P Y F E+++ A
Sbjct: 6 RSLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALS 65
Query: 61 AIRGRDGYNFDGCRLRVELA 80
A+R +G F G LRV+ A
Sbjct: 66 AMRNLNGREFSGRALRVDNA 85
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 43/77 (55%), Gaps = 3/77 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIR 63
R + V +P+ + E ++ LF +YG I +++ + + Y FV+F++ A+ AI
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 64 GRDGYNFDGCRLRVELA 80
G +G+N RL+V LA
Sbjct: 103 GLNGFNILNKRLKVALA 119
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.1 bits (105), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 26 LFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGRDGYNFDGCRLRVELA 80
+F KYGR+ D+ + + + FV F + RDAEDA+ DG DG LRV++A
Sbjct: 90 VFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 44.7 bits (104), Expect = 7e-05, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGR 65
S ++VGN+ E+ F +YG +++ ++ Y FV E A DA +AIRG
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD-----YAFVHMERAEDAVEAIRGL 64
Query: 66 DGYNFDGCRLRVELA 80
D F G R+ V+L+
Sbjct: 65 DNTEFQGKRMHVQLS 79
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDAI 62
SR +Y+G++P D E ++ DL G ++++++ P R Y F+EF + + A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 63 RGRDGYNF 70
R +GY
Sbjct: 62 RNLNGYQL 69
>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 = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDAI 62
SR +Y+G++P D E ++ DL G ++++++ P R Y F+EF + + A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 63 RGRDGYNF 70
R +GY
Sbjct: 63 RNLNGYQL 70
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 41/73 (56%), Gaps = 6/73 (8%)
Query: 9 IYVGNLPS-DIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDG 67
+++GNL + +++ +VE +F KYG+I+ + + FV++ N R+A A+ G DG
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVH-----KGFAFVQYVNERNARAAVAGEDG 72
Query: 68 YNFDGCRLRVELA 80
G L + LA
Sbjct: 73 RMIAGQVLDINLA 85
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
++ V NL + +F KYGR+ D+ + + + FV F + RDAEDA+
Sbjct: 49 SLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDA 108
Query: 65 RDGYNFDGCRLRVELA 80
DG DG LRV++A
Sbjct: 109 MDGAVLDGRELRVQMA 124
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 3/68 (4%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDAI 62
SR +Y+G++P D E ++ DL G ++++++ P R Y F+EF + + A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 63 RGRDGYNF 70
R +GY
Sbjct: 64 RNLNGYQL 71
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 38/68 (55%), Gaps = 4/68 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKI----PPRPPCYCFVEFENARDAEDAIRG 64
+++G L ++ + + ++F YG+I I++ + P Y +VEFEN +AE A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 65 RDGYNFDG 72
DG DG
Sbjct: 67 MDGGQIDG 74
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 39/73 (53%), Gaps = 6/73 (8%)
Query: 9 IYVGNLPSD-IREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDG 67
+++GNL + +++ +VE +F KYGR+ + Y FV++ N R A A+ G +G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH-----KGYAFVQYSNERHARAAVLGENG 84
Query: 68 YNFDGCRLRVELA 80
G L + +A
Sbjct: 85 RVLAGQTLDINMA 97
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPR-PPCYCFVEFENARDAEDAIRGR 65
+ ++V N+P R+ ++ +F ++G+ILD+E+ R + FV FEN+ DA+ A
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 89
Query: 66 DGYNFDGCRLRVELA 80
G +G ++ V A
Sbjct: 90 HGTVVEGRKIEVNNA 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 43.1 bits (100), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 1/75 (1%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPR-PPCYCFVEFENARDAEDAIRGR 65
+ ++V N+P R+ ++ +F ++G+ILD+E+ R + FV FEN+ DA+ A
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKL 75
Query: 66 DGYNFDGCRLRVELA 80
G +G ++ V A
Sbjct: 76 HGTVVEGRKIEVNNA 90
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/68 (38%), Positives = 39/68 (57%), Gaps = 2/68 (2%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP-RPPC-YCFVEFENARDAEDAIR 63
S T+YVGNL E ++ +LF K G I I + + + C +CFVE+ + DAE+A+R
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 64 GRDGYNFD 71
+G D
Sbjct: 78 YINGTRLD 85
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 40/74 (54%), Gaps = 3/74 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPP---CYCFVEFENARDAEDAIRGR 65
+++ +LP + + ++ F +G ++ ++ I + C+ FV F+N A+ AI+
Sbjct: 43 LFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAM 102
Query: 66 DGYNFDGCRLRVEL 79
+G+ RL+V+L
Sbjct: 103 NGFQVGTKRLKVQL 116
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 37/67 (55%), Gaps = 3/67 (4%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
T+YVGNL E ++ +LF K G I I + K+ +CFVE+ + DAE+A+R
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRY 100
Query: 65 RDGYNFD 71
+G D
Sbjct: 101 INGTRLD 107
>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 = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 5 FSRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDA 61
F+R IYV ++ D+ + +++ +F +G+I L P + Y F+E+E A+ ++DA
Sbjct: 125 FNR-IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDA 183
Query: 62 IRGRDGYNFDGCRLRV 77
+ + ++ G LRV
Sbjct: 184 VSSMNLFDLGGQYLRV 199
>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 = 41.6 bits (96), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>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 = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGR 65
+YV LP + + E+E LF +YGRI+ + ++ F+ F+ +AE+AI+G
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 66 DGYNFDGC 73
+G G
Sbjct: 151 NGQKPSGA 158
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
R +YVG L ++ + + F +G I DI++ + + + FVEFE A DA AI
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 64 GRDGYNFDGCRLRVELA 80
+ G +RV LA
Sbjct: 73 NMNESELFGRTIRVNLA 89
>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 = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 3/75 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILD---IELKIPPRPPCYCFVEFENARDAEDAIRGR 65
++VG+L +I +++ F +GRI D ++ + Y FV F N DAE+AI+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 66 DGYNFDGCRLRVELA 80
G G ++R A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>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 = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
++VGNLP DI E E+ LF KYG+ ++ + + + F+ E AE A D
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 74
Query: 69 NFDGCRLRVELA 80
G +LRV A
Sbjct: 75 PLRGKQLRVRFA 86
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 37/72 (51%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGR 65
+R +Y+ NLP I E+ D+F KYG I I + P +V +E+ DA++A+
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 66 DGYNFDGCRLRV 77
G+N L V
Sbjct: 68 SGFNVSNRYLVV 79
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 43/78 (55%), Gaps = 4/78 (5%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIR 63
R IYVGNL +V++LF ++G++ +++L + +P + FVE + +E AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIA 60
Query: 64 GRDGYNFDGCRLRVELAH 81
D +F G +RV A+
Sbjct: 61 KLDNTDFMGRTIRVTEAN 78
>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 = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 5 FSRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDA 61
F+R IYV ++ D+ + +++ +F +G+I L P + Y F+E+E A+ ++DA
Sbjct: 110 FNR-IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 168
Query: 62 IRGRDGYNFDGCRLRV 77
+ + ++ G LRV
Sbjct: 169 VSSMNLFDLGGQYLRV 184
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 20 EYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGRDGYNFDGCRLR 76
E ++ ++F KYG I D+ + + R + FV FEN DA++A +G DG R+R
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 119
Query: 77 VELA 80
V+ +
Sbjct: 120 VDFS 123
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSAT 65
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F R++ A
Sbjct: 66 NALRSXQGFPFYDKPXRIQYA 86
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSAT 66
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F R++ A
Sbjct: 67 NALRSXQGFPFYDKPXRIQYA 87
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 6 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 65
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 66 NALRSMQGFPFYDKPMRIQYA 86
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 2 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 61
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 62 NALRSMQGFPFYDKPMRIQYA 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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 3 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 62
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 63 NALRSMQGFPFYDKPMRIQYA 83
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPR---PPCYCFVEFENARDAEDAIRG 64
+++ +LP + + ++ +F +G ++ ++ I + C+ FV ++N A+ AI+
Sbjct: 27 NLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAIQS 86
Query: 65 RDGYNFDGCRLRVEL 79
+G+ RL+V+L
Sbjct: 87 MNGFQIGMKRLKVQL 101
>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 = 40.0 bits (92), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 4 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 63
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 64 NALRSMQGFPFYDKPMRIQYA 84
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
++VGNLP DI E E+ LF KYG+ ++ + + + F+ E AE A D
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIH---KDKGFGFIRLETRTLAEIAKVELDNM 81
Query: 69 NFDGCRLRVELA 80
G +LRV A
Sbjct: 82 PLRGKQLRVRFA 93
>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 = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 1 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSAT 60
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 61 NALRSMQGFPFYDKPMRIQYA 81
>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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 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 = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 43/76 (56%), Gaps = 4/76 (5%)
Query: 5 FSRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDA 61
F+R IYV ++ D+ + +++ +F +G+I L P + Y F+E+E A+ ++DA
Sbjct: 109 FNR-IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDA 167
Query: 62 IRGRDGYNFDGCRLRV 77
+ + ++ G LRV
Sbjct: 168 VSSXNLFDLGGQYLRV 183
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 39.7 bits (91), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 7 RPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSAT 66
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F +R++ A
Sbjct: 67 NALRSMQGFPFYDKPMRIQYA 87
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
R +YVG L ++ + + F +G I DI++ + + + FVEFE A DA AI
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 64 GRDGYNFDGCRLRVELA 80
+ G +RV LA
Sbjct: 124 NMNESELFGRTIRVNLA 140
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 20 EYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGRDGYNFDGCRLR 76
E ++ ++F KYG I D+ + + R + FV FEN DA++A +G DG R+R
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 77 VELA 80
V+ +
Sbjct: 89 VDFS 92
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRGR 65
+YV LP + + E+E LF +YGRI+ + + F+ F+ +AE+AI+G
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 66 DG 67
+G
Sbjct: 153 NG 154
Score = 30.0 bits (66), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 35/85 (41%), Gaps = 15/85 (17%)
Query: 123 SEYRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGT 182
S+ +IV LP + + + K GD+ ++ RD QS
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLG--------------- 47
Query: 183 YGVVDYTNPEDMKYAIRKLDDTEFR 207
YG V+Y++P D AI L+ + +
Sbjct: 48 YGFVNYSDPNDADKAINTLNGLKLQ 72
>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 = 39.3 bits (90), Expect = 0.002, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
R +YVG L ++ + + F +G I DI++ + + + FVEFE A DA AI
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 64 GRDGYNFDGCRLRVELA 80
+ G +RV LA
Sbjct: 68 NMNESELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
R +YVG L ++ + + F +G I DI++ + + + FVEFE A DA AI
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 64 GRDGYNFDGCRLRVELA 80
+ G +RV LA
Sbjct: 66 NMNESELFGRTIRVNLA 82
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 39.3 bits (90), Expect = 0.003, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 37/72 (51%), Gaps = 5/72 (6%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
I+VGN+ + E+ LF + GR+++ ++ Y FV E DA+ AI +G
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKD-----YAFVHMEKEADAKAAIAQLNGK 66
Query: 69 NFDGCRLRVELA 80
G R+ VEL+
Sbjct: 67 EVKGKRINVELS 78
>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 = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 25/77 (32%), Positives = 38/77 (49%), Gaps = 3/77 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
R +YVG L ++ + + F +G I DI++ + + + FVEFE A DA AI
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 64 GRDGYNFDGCRLRVELA 80
+ G +RV LA
Sbjct: 63 NMNESELFGRTIRVNLA 79
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 42/81 (51%), Gaps = 4/81 (4%)
Query: 4 RFSRTIYVGNLPSDIREYEVED----LFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
R + TIY+ NL I++ E++ +F ++G+ILDI + + FV F+ A
Sbjct: 4 RPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSAT 63
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
+A+R G+ F R++ A
Sbjct: 64 NALRSXQGFPFYDKPXRIQYA 84
>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 = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIR 63
+T++V + D E ++ F YG I I + K +P Y F+E+E+ RD A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 64 GRDGYNFDGCRLRVEL 79
DG DG R+ V++
Sbjct: 163 HADGKKIDGRRVLVDV 178
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 36/64 (56%), Gaps = 3/64 (4%)
Query: 20 EYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGRDGYNFDGCRLR 76
E ++ ++F KYG I D+ + + R + FV FEN DA++A +G DG R+R
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 85
Query: 77 VELA 80
V+ +
Sbjct: 86 VDFS 89
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILD---IELKIPPRPPCYCFVEFENARDAEDAIRGR 65
++VG+L +I +++ F +G+I D ++ + Y FV F N DAE+AI
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 66 DGYNFDGCRLRVELA 80
G G ++R A
Sbjct: 78 GGQWLGGRQIRTNWA 92
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 41/75 (54%), Gaps = 4/75 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPP---CYCFVEFENARDAEDAIRGR 65
+++G L + E ++ +F K+G I ++ L I R + F+ FEN DA++A +
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLL-IKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 66 DGYNFDGCRLRVELA 80
+G + G ++VE A
Sbjct: 69 NGKSLHGKAIKVEQA 83
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGR 65
+R +Y+ NLP I E+ D+F KYG I I + P +V +E+ DA++A
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 66 DGYN 69
G+N
Sbjct: 78 SGFN 81
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRGR 65
+Y+ LP + + +VED+F ++GRI++ + + F+ F+ +AE+AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 66 DGYNFDGC 73
+G+ G
Sbjct: 151 NGHKPPGS 158
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 36/68 (52%), Gaps = 3/68 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRGR 65
+Y+ LP + + +VED+F ++GRI++ + + F+ F+ +AE+AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 66 DGYNFDGC 73
+G+ G
Sbjct: 151 NGHKPPGS 158
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 38.5 bits (88), Expect = 0.005, Method: Composition-based stats.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRGR 65
+YV LP + + E+E LF +YGRI+ + + F+ F+ +AE+AI+G
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 66 DG 67
+G
Sbjct: 64 NG 65
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 20 EYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGRDGYNFDGCRLR 76
E ++ ++F KYG I D+ + + R + FV FEN DA++A +G DG R+R
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 77 V 77
V
Sbjct: 89 V 89
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGR 65
+R +Y+ NLP I E+ D+F KYG I I + P +V +E+ DA++A
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 66 DGYN 69
G+N
Sbjct: 72 SGFN 75
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 38/76 (50%), Gaps = 3/76 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL--KIPPRPPCYCFVEFENARDAEDAIRG 64
RT+YVGNL D+ E + LF + G ++ + P YCFVEF RDA A+
Sbjct: 16 RTLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAA 74
Query: 65 RDGYNFDGCRLRVELA 80
+G G ++V A
Sbjct: 75 MNGRKILGKEVKVNWA 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 38.1 bits (87), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP--RPPCYCFVEFENARDAEDAIRG 64
R +YVGNL I E ++ F G I +I++ I + Y FVE+ + DA A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 65 RDGYNFDGCRLRVELA 80
+G + +++ A
Sbjct: 61 LNGKQIENNIVKINWA 76
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 22/85 (25%)
Query: 125 YRVIVRGLPSSASWQDLKDHMRKAG-DVCFAEV-SRDSEGWQSPAMILLTLNFLCVYSGT 182
YR+ ++ LP SWQDLKD R+ + F+ V +RD +G
Sbjct: 7 YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-------------------- 46
Query: 183 YGVVDYTNPEDMKYAIRKLDDTEFR 207
G +++ + E + A+ +L++ EFR
Sbjct: 47 TGALEFPSEEILVEALERLNNIEFR 71
>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 = 37.7 bits (86), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIR 63
+T++V + D E ++ F YG I I + K +P Y F+E+E+ RD A +
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYK 162
Query: 64 GRDGYNFDGCRLRVEL 79
DG DG R+ V++
Sbjct: 163 HADGKKIDGRRVLVDV 178
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 41/85 (48%), Gaps = 22/85 (25%)
Query: 125 YRVIVRGLPSSASWQDLKDHMRKAG-DVCFAEV-SRDSEGWQSPAMILLTLNFLCVYSGT 182
YR+ ++ LP SWQDLKD R+ + F+ V +RD +G
Sbjct: 29 YRITMKNLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-------------------- 68
Query: 183 YGVVDYTNPEDMKYAIRKLDDTEFR 207
G +++ + E + A+ +L++ EFR
Sbjct: 69 TGALEFPSEEILVEALERLNNIEFR 93
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 33/70 (47%), Gaps = 3/70 (4%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDG 67
T Y+GN+P E ++ LF +G ILD K P C CF++++ A I
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILD--FKHYPEKGC-CFIKYDTHEQAAVCIVALAN 85
Query: 68 YNFDGCRLRV 77
+ F G LR
Sbjct: 86 FPFQGRNLRT 95
>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 = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
+YV NLP I + +++ +F KYG I+ + K+ RP FV + +A++AI
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 72
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 37.4 bits (85), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 38/72 (52%), Gaps = 3/72 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIRGR 65
+YVG+L +I E + +F +GRI I+L + R Y F+ F ++ A+ A+
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 66 DGYNFDGCRLRV 77
+G+ G ++V
Sbjct: 89 NGFELAGRPMKV 100
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 37.0 bits (84), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 6/76 (7%)
Query: 3 GRFSRT-IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDA 61
G S T ++V P D++E E+ ++F +G + ++++ + FVEFE A A A
Sbjct: 27 GELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKA 81
Query: 62 IRGRDGYNFDGCRLRV 77
I G +F L V
Sbjct: 82 IEEVHGKSFANQPLEV 97
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
+YV NLP I + +++ +F KYG I+ + K+ RP FV + +A++AI
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 27.3 bits (59), Expect = 10.0, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 3/76 (3%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPP---CYCFVEFENARDAEDAIRGR 65
+ V LP D+ + E+ LF G I + + Y FV+F + D++ AI+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 66 DGYNFDGCRLRVELAH 81
+G RL+V A
Sbjct: 66 NGITVRNKRLKVSYAR 81
>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 = 37.0 bits (84), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
+YV NLP I + +++ +F KYG I+ + K+ RP FV + +A++AI
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 159
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 3/76 (3%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
T+YVG L + E + +LF + G +++ + ++ + Y FVEF + DA+ AI+
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 65 RDGYNFDGCRLRVELA 80
D G +RV A
Sbjct: 77 MDMIKLYGKPIRVNKA 92
>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 = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGR 65
+R + + NLP I E+ D+F KYG I I + P +V +E+ DA++A
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 66 DGYN 69
G+N
Sbjct: 78 SGFN 81
>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 = 35.4 bits (80), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 36/75 (48%), Gaps = 2/75 (2%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKI--PPRPPCYCFVEFENARDAEDAIRGRD 66
+++ LP + E+E++ +G + D+ L +P +VE+EN A A+ D
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 67 GYNFDGCRLRVELAH 81
G ++V +++
Sbjct: 80 GMTIKENIIKVAISN 94
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 36/72 (50%), Gaps = 3/72 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
++VGNLP+DI E + + LF +YG ++ + R + F+ E+ AE A DG
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFIN---RDRGFGFIRLESRTLAEIAKAELDGT 81
Query: 69 NFDGCRLRVELA 80
LR+ A
Sbjct: 82 ILKSRPLRIRFA 93
>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 = 35.0 bits (79), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
++YVG+L D+ E + + F G IL I + I R Y +V F+ DAE A+
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-- 69
Query: 65 RDGYNFD 71
D NFD
Sbjct: 70 -DTMNFD 75
>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 = 34.7 bits (78), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 34/67 (50%), Gaps = 6/67 (8%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
++YVG+L D+ E + + F G IL I + I R Y +V F+ DAE A+
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL-- 74
Query: 65 RDGYNFD 71
D NFD
Sbjct: 75 -DTMNFD 80
>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 = 34.3 bits (77), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 38/88 (43%), Gaps = 11/88 (12%)
Query: 3 GRFSRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---------YCFVEFE 53
G +R +YVGN+P I E + D F R+ + + P P + F+EF
Sbjct: 1 GAMARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFR 59
Query: 54 NARDAEDAIRGRDGYNFDGCRLRVELAH 81
+ + A+ DG F G L++ H
Sbjct: 60 SVDETTQAM-AFDGIIFQGQSLKIRRPH 86
Score = 28.5 bits (62), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
+ +++G LP+ + + +V++L +G + L Y F E+ + + AI
Sbjct: 114 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 173
Query: 63 RGRDGYNFDGCRLRVELA 80
G +G +L V+ A
Sbjct: 174 AGLNGMQLGDKKLLVQRA 191
>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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
+ I+VG + D E+ + D F +YG+I IE+ + + FV F++ D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 163
Query: 64 GRDGYNFDG--CRLRVELA 80
+ + +G C +R L+
Sbjct: 164 IQKYHTVNGHNCEVRKALS 182
>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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
+ I+VG + D E+ + D F +YG+I IE+ + + FV F++ D+ D I
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 162
Query: 64 GRDGYNFDG--CRLRVELA 80
+ + +G C +R L+
Sbjct: 163 IQKYHTVNGHNCEVRKALS 181
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 41/79 (51%), Gaps = 6/79 (7%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIR 63
+ I+VG + D E+ + D F +YG+I IE+ + + + FV F++ D+ D I
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 164
Query: 64 GRDGYNFDG--CRLRVELA 80
+ + +G C +R L+
Sbjct: 165 IQKYHTVNGHNCEVRKALS 183
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
+ I+VG + D E+ + D F +YG+I IE+ + + FV F++ D+ D I
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 156
Query: 64 GRDGYNFDG--CRLRVELA 80
+ + +G C +R L+
Sbjct: 157 IQKYHTVNGHNCEVRKALS 175
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 8/62 (12%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL-----KIPPRPPCYCFVEF---ENARDAED 60
++VG +P E ++ +LF +YG + +I + + PP+ CFV F + A +A++
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 61 AI 62
A+
Sbjct: 66 AL 67
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDG 67
T+Y G + S + + + F +G+I++I + P + Y FV F A AI +G
Sbjct: 27 TVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-FPEKG--YSFVRFSTHESAAHAIVSVNG 83
Query: 68 YNFDG 72
+G
Sbjct: 84 TTIEG 88
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
+ I+VG + D E+ + D F +YG+I IE+ + + FV F++ D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 163
Query: 64 GRDGYNFDG--CRLRVELA 80
+ + +G C +R L+
Sbjct: 164 IQKYHTVNGHNCEVRKALS 182
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 33.5 bits (75), Expect = 0.14, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 5/69 (7%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIRGRDGY 68
++V P D++E E+ ++F +G + ++++ + FVEFE A A AI G
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKIL-----NGFAFVEFEEAESAAKAIEEVHGK 61
Query: 69 NFDGCRLRV 77
+F L V
Sbjct: 62 SFANQPLEV 70
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu
Rna
Length = 88
Score = 33.5 bits (75), Expect = 0.15, Method: Composition-based stats.
Identities = 17/58 (29%), Positives = 31/58 (53%), Gaps = 5/58 (8%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL-----KIPPRPPCYCFVEFENARDAEDA 61
++VG +P E ++ +LF +YG + +I + + PP+ CFV F + A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEA 63
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 6/79 (7%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKI---PPRPPCYCFVEFENARDAEDAIR 63
+ I+VG + D E+ + D F +YG+I IE+ + + FV F++ D+ D I
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDD-HDSVDKIV 161
Query: 64 GRDGYNFDG--CRLRVELA 80
+ + +G C +R L+
Sbjct: 162 IQKYHTVNGHNCEVRKALS 180
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 22/75 (29%), Positives = 37/75 (49%), Gaps = 3/75 (4%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
S +YVG+L +I E + +F +G+I +I L R Y F+ F ++ A A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 63 RGRDGYNFDGCRLRV 77
+G+ G +RV
Sbjct: 65 EQLNGFELAGRPMRV 79
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 35/62 (56%), Gaps = 8/62 (12%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL-----KIPPRPPCYCFVEF---ENARDAED 60
++VG +P E ++ +LF +YG + +I + + PP+ CFV F + A +A++
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 61 AI 62
A+
Sbjct: 78 AL 79
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 31/57 (54%), Gaps = 3/57 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
I+VG +P + E E+ + F K+G + ++ + RP + F+ FE+ + + A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 32.7 bits (73), Expect = 0.21, Method: Composition-based stats.
Identities = 16/54 (29%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
S ++VG D+ E E+ + F +YG ++D+ + P R + FV F + + A+
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFR--AFAFVTFADDQIAQ 56
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 1/75 (1%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYC-FVEFENARDAEDAIRG 64
S I+V NLP D ++D F + G +L ++K+ C V+FE+ AE A R
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRM 64
Query: 65 RDGYNFDGCRLRVEL 79
+G G + V +
Sbjct: 65 MNGMKLSGREIDVRI 79
Score = 29.6 bits (65), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 34/80 (42%), Gaps = 17/80 (21%)
Query: 127 VIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGTYGVV 186
+ VR LP +W+ LKD + G V +A++ ++ S GVV
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG-----------------KSKGCGVV 50
Query: 187 DYTNPEDMKYAIRKLDDTEF 206
+ +PE + A R ++ +
Sbjct: 51 KFESPEVAERACRMMNGMKL 70
>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 = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 8/61 (13%)
Query: 10 YVGNLPSDIREYEVEDLFYKYGRILDIEL-----KIPPRPPCYCFVEF---ENARDAEDA 61
+VG +P E ++ +LF +YG + +I + + PP+ CFV F + A +A++A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 62 I 62
+
Sbjct: 67 L 67
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 11/85 (12%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---------YCFVEFENAR 56
+R +YVGN+P I E + D F R+ + + P P + F+EF +
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 57 DAEDAIRGRDGYNFDGCRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 63 ETTQAM-AFDGIIFQGQSLKIRRPH 86
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
+ +++G LP+ + + +V++L +G + L Y F E+ + + AI
Sbjct: 94 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 153
Query: 63 RGRDGYNFDGCRLRVELA 80
G +G +L V+ A
Sbjct: 154 AGLNGMQLGDKKLLVQRA 171
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRG 64
T++VG + + E E+ F +YG + ++++ I R Y FV F N D + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 65 RDGYNFDGCRLRV 77
+ NF G +L++
Sbjct: 70 Q--INFHGKKLKL 80
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 39/78 (50%), Gaps = 9/78 (11%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP----RPPCYCFVEFENARDAEDA 61
S+T+ + NL E ++++F K I K+P + Y F+EF + DA++A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFI-----KVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 62 IRGRDGYNFDGCRLRVEL 79
+ + +G +R+EL
Sbjct: 70 LNSCNKREIEGRAIRLEL 87
>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 = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 11/85 (12%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---------YCFVEFENAR 56
+R +YVGN+P I E + D F R+ + + P P + F+EF +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 57 DAEDAIRGRDGYNFDGCRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 65 ETTQAM-AFDGIIFQGQSLKIRRPH 88
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/78 (21%), Positives = 35/78 (44%), Gaps = 3/78 (3%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAI 62
+ +++G LP+ + + +V++L +G + L Y F E+ + + AI
Sbjct: 96 AHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAI 155
Query: 63 RGRDGYNFDGCRLRVELA 80
G +G +L V+ A
Sbjct: 156 AGLNGMQLGDKKLLVQRA 173
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/81 (22%), Positives = 35/81 (43%), Gaps = 6/81 (7%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC------YCFVEFENARDAE 59
S +++ NL E ++ +F K G I + + FVE++ A+
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 60 DAIRGRDGYNFDGCRLRVELA 80
A++ G+ DG +L V ++
Sbjct: 65 KALKQLQGHTVDGHKLEVRIS 85
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 14/34 (41%), Positives = 19/34 (55%)
Query: 47 YCFVEFENARDAEDAIRGRDGYNFDGCRLRVELA 80
Y FV F N DA +A++ +G DG + V LA
Sbjct: 53 YAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLA 86
>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 = 32.3 bits (72), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 21/76 (27%), Positives = 40/76 (52%), Gaps = 4/76 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRGR 65
I+VG + D+R E E+ F ++G I+D +L K + + FV +++A DA D +
Sbjct: 90 IFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSA-DAVDRVCQN 148
Query: 66 DGYNFDGCRLRVELAH 81
+F ++ ++ A
Sbjct: 149 KFIDFKDRKIEIKRAE 164
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/58 (24%), Positives = 29/58 (50%), Gaps = 3/58 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDAIR 63
+++G L D E + + F KYG + D+++ P R + F+ FE ++ ++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 32.0 bits (71), Expect = 0.38, Method: Composition-based stats.
Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDA 61
T+YVG L I E ++ + FY++G I I + R C F++F + AE A
Sbjct: 14 TLYVGGLGDTITETDLRNHFYQFGEIRTI--TVVQRQQC-AFIQFATRQAAEVA 64
>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 = 32.0 bits (71), Expect = 0.39, Method: Composition-based stats.
Identities = 18/66 (27%), Positives = 35/66 (53%), Gaps = 4/66 (6%)
Query: 10 YVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDAIRGRD 66
+VG L D + +++D F K+G ++D +K P R + F+ F++A E + ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 67 GYNFDG 72
+ DG
Sbjct: 75 -HRLDG 79
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 1/72 (1%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYC-FVEFENARDAEDAIRGRDG 67
I+V NLP D ++D F + G +L ++K+ C V+FE+ AE A R +G
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMNG 70
Query: 68 YNFDGCRLRVEL 79
G + V +
Sbjct: 71 MKLSGREIDVRI 82
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 17/81 (20%)
Query: 126 RVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGTYGV 185
++ VR LP +W+ LKD + G V +A++ ++ S GV
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENG-----------------KSKGCGV 52
Query: 186 VDYTNPEDMKYAIRKLDDTEF 206
V + +PE + A R ++ +
Sbjct: 53 VKFESPEVAERACRMMNGMKL 73
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 31.6 bits (70), Expect = 0.49, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRG 64
T++VG + + E E+ F +YG + ++++ I R Y FV F N D + +
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 70
Query: 65 RDGYNFDGCRLRV 77
+ NF G +L++
Sbjct: 71 Q--INFHGKKLKL 81
>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 = 0.56, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 6/73 (8%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---YCFVEFENARDAEDAIRG 64
T++VG + + E E+ F +YG + ++++ I R Y FV F N D + +
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKI-ITDRTGVSKGYGFVSFYNDVDVQKIVES 69
Query: 65 RDGYNFDGCRLRV 77
+ NF G +L++
Sbjct: 70 Q--INFHGKKLKL 80
>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 = 31.6 bits (70), Expect = 0.58, Method: Composition-based stats.
Identities = 15/61 (24%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPP---RPPCYCFVEFENARDAEDAIRGR 65
+++G L D + +++D F K+G ++D LK+ P R + FV F+ + + + +
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 66 D 66
+
Sbjct: 62 E 62
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 0.62, Method: Composition-based stats.
Identities = 14/51 (27%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAE 59
++VG D+ E++ F +YG ++D+ + P R + FV F + + A+
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFR--AFAFVTFADDKVAQ 62
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 31.2 bits (69), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 35/74 (47%), Gaps = 4/74 (5%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRI-LDIELKIPPRPPCYCFVEFENARDAEDAIRGRDG 67
+YVGNLP D R +++ + G + L + + P R F+ + ++ A+ A+ G
Sbjct: 22 VYVGNLPRDARVSDLKRALRELGSVPLRLTWQGPRR---RAFLHYPDSAAAQQAVSCLQG 78
Query: 68 YNFDGCRLRVELAH 81
LRV LA
Sbjct: 79 LRLGTDTLRVALAR 92
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 30.8 bits (68), Expect = 0.87, Method: Composition-based stats.
Identities = 23/85 (27%), Positives = 37/85 (43%), Gaps = 11/85 (12%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---------YCFVEFENAR 56
+R +YVGN+P I E + D F R+ + + P P + F+EF +
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRSVD 59
Query: 57 DAEDAIRGRDGYNFDGCRLRVELAH 81
+ A+ DG F G L++ H
Sbjct: 60 ETTQAM-AFDGIIFQGQSLKIRRPH 83
>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 = 30.8 bits (68), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 4 RFSRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL-KIPPRPPCYCFVEFENARDAEDAI 62
R +RT+ NL +I E E++++F L+I L + ++EF++ DAE +
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFED---ALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 153
Query: 63 RGRDGYNFDG 72
+ G DG
Sbjct: 154 EEKQGAEIDG 163
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 30.0 bits (66), Expect = 1.4, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 34/68 (50%), Gaps = 2/68 (2%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIEL--KIPPRPPCYCFVEFENARDAEDAIRG 64
RT++VGNL + +RE + +LF + G + + + +P + FV F++ AI
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 65 RDGYNFDG 72
+G G
Sbjct: 77 LNGIRLYG 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 = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 17/76 (22%), Positives = 36/76 (47%), Gaps = 3/76 (3%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
T+YV NLP + ++ +F KYG+++ + + K + F+ F + A++ R
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 65 RDGYNFDGCRLRVELA 80
+ G ++ +A
Sbjct: 78 INNKQLFGRVIKASIA 93
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 29.6 bits (65), Expect = 2.1, Method: Composition-based stats.
Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 23 VEDLFYKYGRIL-DIELKIPPRPPCYCFVEFENARDAEDAIRGRDGYNFD 71
+ +F K+G+I D + + Y F+E+ + A DA++ DGY D
Sbjct: 24 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLD 73
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 29.3 bits (64), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 20/33 (60%)
Query: 127 VIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRD 159
+IV GLP + QDLK++ G+V +V +D
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKD 50
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 2/69 (2%)
Query: 4 RFSRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPCYCFVEFENARDAEDAIR 63
R +RT+ NLP + + E++++F I + + ++EF+ DAE
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSK--DGKSKGIAYIEFKTEADAEKTFE 148
Query: 64 GRDGYNFDG 72
+ G DG
Sbjct: 149 EKQGTEIDG 157
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 23 VEDLFYKYGRIL-DIELKIPPRPPCYCFVEFENARDAEDAIRGRDGYNFDGCR-LRVEL 79
+ +F K+G+I D + + Y F+E+ + A DA++ DGY D RV L
Sbjct: 38 IHKIFSKFGKITNDFYPEEDGKTKGYIFLEYASPAHAVDAVKNADGYKLDKQHTFRVNL 96
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 28.9 bits (63), Expect = 3.1, Method: Composition-based stats.
Identities = 22/81 (27%), Positives = 36/81 (44%), Gaps = 11/81 (13%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC---------YCFVEFENAR 56
+R +YVGN+P I E + D F R+ + + P P + F+EF +
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLT-QAPGNPVLAVQINQDKNFAFLEFRSVD 64
Query: 57 DAEDAIRGRDGYNFDGCRLRV 77
+ A+ DG F G L++
Sbjct: 65 ETTQAM-AFDGIIFQGQSLKI 84
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 21/36 (58%)
Query: 1 MSGRFSRTIYVGNLPSDIREYEVEDLFYKYGRILDI 36
M G SR +++ LP ++ E EV L +G++ +I
Sbjct: 10 MDGAPSRVLHIRKLPGEVTETEVIALGLPFGKVTNI 45
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 28.9 bits (63), Expect = 3.6, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 33/80 (41%), Gaps = 15/80 (18%)
Query: 123 SEYRVIVRGLPSSASWQDLKDHMRKAGDVCFAEVSRDSEGWQSPAMILLTLNFLCVYSGT 182
S+ +IV LP + + + K GD+ ++ RD QS
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLG--------------- 47
Query: 183 YGVVDYTNPEDMKYAIRKLD 202
YG V+Y++P D AI L+
Sbjct: 48 YGFVNYSDPNDADKAINTLN 67
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.5 bits (62), Expect = 5.1, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 4 RFSRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL-KIPPRPPCYCFVEFENARDAEDAI 62
R +RT+ NL +I E E++++F L+I L + ++EF++ DAE +
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFED---ALEIRLVSQDGKSKGIAYIEFKSEADAEKNL 70
Query: 63 RGRDGYNFDG 72
+ G DG
Sbjct: 71 EEKQGAEIDG 80
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 5/77 (6%)
Query: 8 TIYVGNLPSDIREYEVEDLFYKYGRILDIEL---KIPPRPPCYCFVEFENARDAEDAIRG 64
T YVGNLP + + ++ D +K I + L K + +C+VEF+ ++A+
Sbjct: 17 TAYVGNLPFNTVQGDI-DAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALT- 74
Query: 65 RDGYNFDGCRLRVELAH 81
DG LRV++A
Sbjct: 75 YDGALLGDRSLRVDIAE 91
>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 = 28.1 bits (61), Expect = 5.6, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 26/50 (52%), Gaps = 3/50 (6%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPP---CYCFVEFE 53
+ I+VG L D E ++ + F +G + IEL + + +CF+ F+
Sbjct: 2 KKIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK 51
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 21/35 (60%)
Query: 4 RFSRTIYVGNLPSDIREYEVEDLFYKYGRILDIEL 38
R +RT++ L + IR ++ED F G++ D+ +
Sbjct: 23 RDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRI 57
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 11/28 (39%), Positives = 18/28 (64%)
Query: 7 RTIYVGNLPSDIREYEVEDLFYKYGRIL 34
R ++VG LP DI E E+ F ++G ++
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLV 36
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 28.1 bits (61), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 30/53 (56%), Gaps = 3/53 (5%)
Query: 14 LPSDIREYEVEDLFYKYGRILDIELKIPPRPPCY---CFVEFENARDAEDAIR 63
L ++RE ++D+ KYG + ++E+ + PR + V F + R A++ ++
Sbjct: 14 LNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGAKETVK 66
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 27.7 bits (60), Expect = 6.9, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 6/67 (8%)
Query: 6 SRTIYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPPC-----YCFVEFENARDAED 60
S I++GNL +I E + D F +G IL KI P Y F+ F + ++
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTP-KIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 61 AIRGRDG 67
AI +G
Sbjct: 64 AIEAMNG 70
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 9/30 (30%), Positives = 21/30 (70%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIEL 38
++VG +P + E +++ LF ++GRI ++ +
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTV 47
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 27.7 bits (60), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 3/75 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPP---CYCFVEFENARDAEDAIRGR 65
+ V LP D+ + E+ LF G I + + Y FV+F + D++ AI+
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 66 DGYNFDGCRLRVELA 80
+G RL+V A
Sbjct: 66 NGITVRNKRLKVSYA 80
>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 = 27.3 bits (59), Expect = 9.3, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 36/75 (48%), Gaps = 3/75 (4%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILD---IELKIPPRPPCYCFVEFENARDAEDAIRGR 65
++VG+L +I + F +GRI D ++ + Y FV F N DAE+AI+
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 66 DGYNFDGCRLRVELA 80
G G ++R A
Sbjct: 69 GGQWLGGRQIRTNWA 83
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 27.3 bits (59), Expect = 9.4, Method: Composition-based stats.
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 9 IYVGNLPSDIREYEVEDLFYKYGRILDIELKIPPRPP---CYCFVEFE 53
I+VG L D E ++ + F +G + IEL + + +CF+ F+
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFK 49
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
0.322 0.140 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,133,011
Number of Sequences: 62578
Number of extensions: 219819
Number of successful extensions: 607
Number of sequences better than 100.0: 148
Number of HSP's better than 100.0 without gapping: 100
Number of HSP's successfully gapped in prelim test: 48
Number of HSP's that attempted gapping in prelim test: 449
Number of HSP's gapped (non-prelim): 169
length of query: 289
length of database: 14,973,337
effective HSP length: 98
effective length of query: 191
effective length of database: 8,840,693
effective search space: 1688572363
effective search space used: 1688572363
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)