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= 046599
(131 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 78.2 bits (191), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 39/72 (54%), Positives = 53/72 (73%), Gaps = 4/72 (5%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGKN 62
+VYVGNL + ++ +LE F +G +RSVWVAR PPG+AF++F+D RDA DA+RELDG+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRT 134
Query: 63 ----GWRVELSH 70
RVELS+
Sbjct: 135 LCGCRVRVELSN 146
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 76.6 bits (187), Expect = 3e-15, Method: Compositional matrix adjust.
Identities = 38/72 (52%), Positives = 53/72 (73%), Gaps = 4/72 (5%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGKN 62
+VYVGNL + ++ +LE F +G +RSVWVAR PPG+AF++F+D RDA DA+R+LDG+
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRT 134
Query: 63 ----GWRVELSH 70
RVELS+
Sbjct: 135 LCGCRVRVELSN 146
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 76.3 bits (186), Expect = 4e-15, Method: Compositional matrix adjust.
Identities = 37/71 (52%), Positives = 52/71 (73%), Gaps = 4/71 (5%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK- 61
+VYVGNL + + +LE F +G +R+VW+AR PPG+AF++F+D RDA+DA+R LDGK
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKV 61
Query: 62 ---NGWRVELS 69
+ RVELS
Sbjct: 62 ICGSRVRVELS 72
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 51.2 bits (121), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/70 (40%), Positives = 45/70 (64%), Gaps = 4/70 (5%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARR--PPGYAFIDFDDYRDAQDAIRELDG 60
R+YVGNL + +D+ED F +G IR + + R P +AF++F+D RDA+DA+ DG
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG 83
Query: 61 --KNGWRVEL 68
+G+R+ +
Sbjct: 84 YDYDGYRLRV 93
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 46.6 bits (109), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 35/66 (53%), Gaps = 6/66 (9%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP------GYAFIDFDDYRDAQDAI 55
S +++GNLD + E+ L D F FGVI R P GYAFI+F + + AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 56 RELDGK 61
++G+
Sbjct: 66 EAMNGQ 71
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP-----GYAFIDFDDYRDAQDAIR 56
+R+YV ++ +S+ D++ F FG I+S +AR P GY FI+++ + +QDA+
Sbjct: 126 NRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVS 185
Query: 57 ELD 59
++
Sbjct: 186 SMN 188
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 37/64 (57%), Gaps = 5/64 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSV---W--VARRPPGYAFIDFDDYRDAQDAI 55
MSRVYVG++ + E + F FG I+S+ W V + G+AF++++ AQ A+
Sbjct: 28 MSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 87
Query: 56 RELD 59
+++
Sbjct: 88 EQMN 91
>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 = 43.9 bits (102), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 38/63 (60%), Gaps = 5/63 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP-----GYAFIDFDDYRDAQDAIR 56
+R+YV ++ +S+ D++ F FG I+S +AR P GY FI+++ + +QDA+
Sbjct: 111 NRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVS 170
Query: 57 ELD 59
++
Sbjct: 171 SMN 173
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSV---W--VARRPPGYAFIDFDDYRDAQDAI 55
M RVYVG++ + E + F FG I+S+ W V + G+AF++++ AQ A+
Sbjct: 13 MCRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLAL 72
Query: 56 RELD 59
+++
Sbjct: 73 EQMN 76
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 43.1 bits (100), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 34/64 (53%), Gaps = 4/64 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRP----PGYAFIDFDDYRDAQDAIREL 58
+++VG L+ + SE D+ F+ FGVI V R P G AF+ F + +AQ AI L
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 59 DGKN 62
G
Sbjct: 77 HGSQ 80
>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 = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 36/60 (60%), Gaps = 5/60 (8%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP-----GYAFIDFDDYRDAQDAI 55
+R+YV ++ +S+ D++ F FG I+S +AR P GY FI+++ + +QDA+
Sbjct: 109 FNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 10/70 (14%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSV---W--VARRPPGYAFIDFDDYRDAQDAIRE 57
RVYVG++ + E + F FG I+S+ W V + G+AF++++ AQ A+ +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 58 -----LDGKN 62
L G+N
Sbjct: 74 XNSVXLGGRN 83
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 37/65 (56%), Gaps = 5/65 (7%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIRE 57
+++VG L +E+ LE F +G I V V + R G+ F+ F++ DA+DA+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 58 LDGKN 62
++GK+
Sbjct: 74 MNGKS 78
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIRE 57
R+YVG+L ++E L F FG I S+ + R GY FI F D A+ A+ +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 58 LDG 60
L+G
Sbjct: 88 LNG 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 40.8 bits (94), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 36/62 (58%), Gaps = 4/62 (6%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA----RRPPGYAFIDFDDYRDAQDAIRELD 59
+YVGNLD ++E L+ F+V G I ++ + + YAF+++ DA A++ L+
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Query: 60 GK 61
GK
Sbjct: 63 GK 64
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRS---VWVARRPP--GYAFIDFDDYRDAQDAIRE 57
++VG+L+ V + L + F+ F S +W + GY F+ F DAQ+A+
Sbjct: 89 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 148
Query: 58 LDGK 61
+ G+
Sbjct: 149 MQGQ 152
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 25/65 (38%), Positives = 33/65 (50%), Gaps = 5/65 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP-----GYAFIDFDDYRDAQDAI 55
M + V NL R S L F +G + V++ R P G+AF+ F D RDAQDA
Sbjct: 13 MITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAE 72
Query: 56 RELDG 60
+DG
Sbjct: 73 AAMDG 77
>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 = 39.7 bits (91), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
++V ++ +E L EF V+G I+ + + + +P GYAFI+++ RD A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 59 DGK--NGWRV 66
DGK +G RV
Sbjct: 165 DGKKIDGRRV 174
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRP----PGYAFIDFDDYRDAQDAIREL 58
+++VG L+ + SE D+ F FG I + R P G AF+ + + +AQ AI L
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 59 DG 60
G
Sbjct: 77 HG 78
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 39/70 (55%), Gaps = 7/70 (10%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
++V ++ +E L EF V+G I+ + + + +P GYAFI+++ RD A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 59 DGK--NGWRV 66
DGK +G RV
Sbjct: 165 DGKKIDGRRV 174
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 39.3 bits (90), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVW-----VARRPPGYAFIDFDDYRDAQDAIRE 57
R++V NL SE DLE F +G + + + ++P G+AF+ F A A E
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 58 LDGK 61
+DG+
Sbjct: 70 VDGQ 73
>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 = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIREL 58
V+VG+L ++ D++ F FG I V + + GY F+ F + DA++AI+++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 59 DGK 61
G+
Sbjct: 78 GGQ 80
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 39/64 (60%), Gaps = 4/64 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPPGYAFIDFDDYRDAQDAIREL 58
++++G L+ +E+ L+ F G I V + + + G+AFI F++ DA++A +++
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 59 DGKN 62
+GK+
Sbjct: 69 NGKS 72
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 38.9 bits (89), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAI 55
M+ + V NL R S L F +G + V++ R G+AF+ F D RDA+DA+
Sbjct: 70 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 129
Query: 56 RELDG 60
+DG
Sbjct: 130 DAMDG 134
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIREL 58
V+VG+L ++ D++ F FG I V + + GY F+ F + DA++AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 59 DGK 61
G+
Sbjct: 78 GGQ 80
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSV-----WVARRPPGYAFIDFDDYRDAQDAI 55
M+ +YVG+L V+E L ++F G I S+ + RR GYA+++F DA+ A+
Sbjct: 10 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 69
Query: 56 RELD 59
++
Sbjct: 70 DTMN 73
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA---RRPPGYAFIDFDDYRDAQDAIRELDG 60
+++ NLD + + L D F FG I S V GY F+ F+ A+ AI +++G
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 160
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 34/65 (52%), Gaps = 5/65 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAI 55
M+ + V NL R S L F +G + V++ R G+AF+ F D RDA+DA+
Sbjct: 47 MTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAM 106
Query: 56 RELDG 60
+DG
Sbjct: 107 DAMDG 111
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 5/64 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSV-----WVARRPPGYAFIDFDDYRDAQDAI 55
M+ +YVG+L V+E L ++F G I S+ + RR GYA+++F DA+ A+
Sbjct: 15 MASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERAL 74
Query: 56 RELD 59
++
Sbjct: 75 DTMN 78
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA---RRPPGYAFIDFDDYRDAQDAIRELDG 60
+++ NLD + + L D F FG I S V GY F+ F+ A+ AI +++G
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 165
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 5/67 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGKN- 62
++V NL + V+E LE F FG + V ++ YAFI FD+ A A+ E++GK+
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERV---KKLKDYAFIHFDERDGAVKAMEEMNGKDL 70
Query: 63 -GWRVEL 68
G +E+
Sbjct: 71 EGENIEI 77
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain
Of Xenopus Laevis Epabp2
Length = 124
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/61 (36%), Positives = 34/61 (55%), Gaps = 6/61 (9%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
VYVGN+D + +DLE F G I + + + P GYA+I+F + R++ DA +
Sbjct: 39 VYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVAM 97
Query: 59 D 59
D
Sbjct: 98 D 98
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 5/73 (6%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP--GYAFIDFDDYRDAQDAIRELDG- 60
+Y+ NL +++ ++ D F +G IR + V P G A++ ++D DA++A+ L G
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGF 70
Query: 61 --KNGWRVELSHN 71
N + V L +N
Sbjct: 71 NVSNRYLVVLYYN 83
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 A Ph 9.0
Length = 115
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 3/60 (5%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA---RRPPGYAFIDFDDYRDAQDAIRELDG 60
+++ NLD + + L D F FG I S V GY F+ F+ A+ AI +++G
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNG 67
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 38.1 bits (87), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
+R++V V E +L + F FG ++ V + G+AF++F++ A AI E+ GK
Sbjct: 32 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGK 88
Query: 62 N 62
+
Sbjct: 89 S 89
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 38.1 bits (87), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 3/63 (4%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVA---RRPPGYAFIDFDDYRDAQDAIRE 57
+ +++ NLD + + L D F FG I S V GY F+ F+ A+ AI +
Sbjct: 11 VGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEK 70
Query: 58 LDG 60
++G
Sbjct: 71 MNG 73
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 39/65 (60%), Gaps = 6/65 (9%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSV--WVARRPP----GYAFIDFDDYRDAQDAI 55
++V++G L V++ + + F +G I+ + V R P GYA+++F++ +A+ A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 56 RELDG 60
+ +DG
Sbjct: 65 KHMDG 69
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ V+VGN+ +E L+D F G + S + +P GY F ++ D A A+
Sbjct: 8 LRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
Query: 56 RELDGK 61
R L+G+
Sbjct: 68 RNLNGR 73
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
+R++V V E +L + F FG ++ V + G+AF++F++ A AI E+ GK
Sbjct: 5 TRLFVRPFPLDVQESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGK 61
Query: 62 N 62
+
Sbjct: 62 S 62
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 5/59 (8%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
++++VG + E +L + F+ FGV+ V + +RP G+ FI F+D + A+
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 30/61 (49%), Gaps = 3/61 (4%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV---ARRPPGYAFIDFDDYRDAQDAIRELDG 60
+YV NLD + + L F FG I S V R G+ F+ F +A A+ E++G
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNG 77
Query: 61 K 61
+
Sbjct: 78 R 78
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 37.4 bits (85), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 4/60 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGY----AFIDFDDYRDAQDAIREL 58
+++VG L + ++ D+ F FG I V R P G AF+ F + +AQ AI L
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 37.0 bits (84), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 34/64 (53%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
S +YVG+L ++E L F FG I ++ + + R GY FI F D A+ A+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 57 ELDG 60
+L+G
Sbjct: 66 QLNG 69
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V + +E D+ D+F +G I+++ + RR GY ++++ Y++AQ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 59 DGKN 62
+G++
Sbjct: 70 NGQD 73
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V + +E D+ D+F +G I+++ + RR GY ++++ Y++AQ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 59 DGKN 62
+G++
Sbjct: 70 NGQD 73
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP--GYAFIDFDDYRDAQDAIRELDGK 61
+Y+ NL +++ ++ D F +G IR + V P G A++ ++D DA++A L G
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 74
Query: 62 N 62
N
Sbjct: 75 N 75
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 34/61 (55%), Gaps = 2/61 (3%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP--GYAFIDFDDYRDAQDAIRELDGK 61
+Y+ NL +++ ++ D F +G IR + V P G A++ ++D DA++A L G
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 62 N 62
N
Sbjct: 81 N 81
>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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V + +E D+ D+F +G I+++ + RR GY ++++ Y++AQ A+ L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 59 DGKN 62
+G++
Sbjct: 72 NGQD 75
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.6 bits (83), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/58 (36%), Positives = 33/58 (56%), Gaps = 3/58 (5%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
++V NL + V+E LE F FG + V ++ YAF+ F+D A A+ E++GK
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERV---KKLKDYAFVHFEDRGAAVKAMDEMNGK 72
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V + +E D+ D+F +G I+++ + RR GY ++++ Y++AQ A+ L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 59 DGKN 62
+G++
Sbjct: 70 NGQD 73
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 2 SRVYVGNLDSR-VSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
SRV++GNL++ V + D+E F +G + V + GYAF+ + + R A+ A+ +G
Sbjct: 28 SRVFIGNLNTALVKKSDVETIFSKYGRVAGCSVHK---GYAFVQYSNERHARAAVLGENG 84
Query: 61 K 61
+
Sbjct: 85 R 85
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 38/61 (62%), Gaps = 4/61 (6%)
Query: 2 SRVYVGNLDSRVSER-DLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
SRV++GNL++ V ++ D+E F +G I V + G+AF+ + + R+A+ A+ DG
Sbjct: 16 SRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHK---GFAFVQYVNERNARAAVAGEDG 72
Query: 61 K 61
+
Sbjct: 73 R 73
>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 = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V + +E D+ D+F +G I+++ + RR GY ++++ Y++AQ A+ L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 59 DGKN 62
+G++
Sbjct: 85 NGQD 88
>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 = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 38/64 (59%), Gaps = 5/64 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V + +E D+ D+F +G I+++ + RR GY ++++ Y++AQ A+ L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 59 DGKN 62
+G++
Sbjct: 86 NGQD 89
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEF--RVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIREL 58
M+++Y+GNL V+ DL F R + V + GYAF+D+ D A AI L
Sbjct: 8 MNKLYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKS---GYAFVDYPDQNWAIRAIETL 64
Query: 59 DGK 61
GK
Sbjct: 65 SGK 67
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 31/58 (53%), Gaps = 3/58 (5%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIREL 58
M ++++GNL +E+++ F +G + + + Y F+ +D A+DAIR L
Sbjct: 8 MVKLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN---YGFVHIEDKTAAEDAIRNL 62
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 35.4 bits (80), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 35/64 (54%), Gaps = 6/64 (9%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPG------YAFIDFDDYRDAQDA 54
S++ V N+ + ++R++ + F FG +++V + ++ G + F+DF +DA+ A
Sbjct: 15 TSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKA 74
Query: 55 IREL 58
L
Sbjct: 75 FNAL 78
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ + V L +++R+L FR G I + + R GYAF+DF D+Q AI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 57 ELDG 60
L+G
Sbjct: 64 VLNG 67
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 58 LDG 60
+ G
Sbjct: 72 MQG 74
>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 = 34.7 bits (78), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 67
Query: 58 LDG 60
+ G
Sbjct: 68 MQG 70
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 58 LDG 60
+ G
Sbjct: 71 MQG 73
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 58 LDG 60
+ G
Sbjct: 72 MQG 74
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 58 LDG 60
+ G
Sbjct: 72 MQG 74
>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 = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 58 LDG 60
+ G
Sbjct: 72 MQG 74
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 68
Query: 58 LDG 60
+ G
Sbjct: 69 MQG 71
>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 = 34.7 bits (78), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 66
Query: 58 LDG 60
+ G
Sbjct: 67 MQG 69
>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 = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65
Query: 58 LDG 60
+ G
Sbjct: 66 MQG 68
>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 = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 58 LDG 60
+ G
Sbjct: 71 MQG 73
>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 = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 58 LDG 60
+ G
Sbjct: 71 MQG 73
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 34.7 bits (78), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ + V L +++R+L FR G I + + R GYAF+DF D+Q AI+
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 57 ELDG 60
L+G
Sbjct: 64 VLNG 67
Score = 32.7 bits (73), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ +YV NL +++ L+ F +G I + R RP G AF+ ++ +AQ+AI
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 57 ELD 59
L+
Sbjct: 150 ALN 152
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFG-VIRSVWVARRPPGY----AFIDFDDYRDAQDAIR 56
+ +Y+ L ++++D+ED F FG +I S + + G AFI FD +A++AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 57 ELDG 60
+G
Sbjct: 149 SFNG 152
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVW-----VARRPPGYAFIDFDDYRDAQDAIR 56
+ + V L +++ +L F G + S VA GY F+++ +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 57 ELDG 60
L+G
Sbjct: 63 TLNG 66
>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 = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ NL+ ++ + +L+ F FG I + V+R + G AF+ F + A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 58 LDG 60
+ G
Sbjct: 71 MQG 73
>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 = 34.7 bits (78), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 35/64 (54%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFG-VIRSVWVARRPPGY----AFIDFDDYRDAQDAIR 56
+ +Y+ L ++++D+ED F FG +I S + + G AFI FD +A++AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 57 ELDG 60
+G
Sbjct: 149 SFNG 152
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVW-----VARRPPGYAFIDFDDYRDAQDAIR 56
+ + V L +++ +L F G + S VA GY F+++ +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 57 ELDG 60
L+G
Sbjct: 63 TLNG 66
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGY----AFIDFDDYRDAQDAIREL 58
++++G + + +E D+ F FG I + R P G AF+ F AQ AI+ +
Sbjct: 97 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 156
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 30/63 (47%), Gaps = 7/63 (11%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPP---GYAFIDFDDYRDAQDAI 55
+++VG + SE+DL + F +G + + V R PP G F+ F + A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 56 REL 58
L
Sbjct: 65 NAL 67
>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 = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGY----AFIDFDDYRDAQDAIR 56
++++G + + +E D+ F FG I + R P G AF+ F AQ AI+
Sbjct: 97 KLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPP---GYAFIDFDDYRDAQDAI 55
+ +VG + SE+DL + F +G + + V R PP G F+ F + A +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 56 REL 58
L
Sbjct: 65 NAL 67
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 34.3 bits (77), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
R++VGNL + ++E D + F +G V++ R G+ FI + A+ A ELDG
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI-NRDRGFGFIRLESRTLAEIAKAELDG 80
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 34.3 bits (77), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGY----AFIDFDDYRDAQDAIREL 58
++++G + + +E D+ F FG I + R P G AF+ F AQ AI+ +
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPP---GYAFIDFDDYR---DAQ 52
+++VG + SE+DL + F +G + + V R PP G F+ F + +AQ
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 53 DAIREL 58
+A+ +
Sbjct: 77 NALHNM 82
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 33.9 bits (76), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 11/68 (16%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVI--------RSVWVARRPPGYAFIDFDDYRDAQD 53
+ +YV L +S++++E F +G I ++ V+R G FI FD +A++
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSR---GVGFIRFDKRIEAEE 58
Query: 54 AIRELDGK 61
AI+ L+G+
Sbjct: 59 AIKGLNGQ 66
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 33.5 bits (75), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 32/69 (46%), Gaps = 10/69 (14%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-------RPPGYAFIDFDDYRDAQ--- 52
+V+VG L + E ++ FR FG + W + P GYAF+ F + Q
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQEESSVQALI 69
Query: 53 DAIRELDGK 61
DA E DGK
Sbjct: 70 DACLEEDGK 78
>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 = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 33/61 (54%), Gaps = 2/61 (3%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP--GYAFIDFDDYRDAQDAIRELDGK 61
+ + NL +++ ++ D F +G IR + V P G A++ ++D DA++A L G
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGF 80
Query: 62 N 62
N
Sbjct: 81 N 81
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 33.5 bits (75), Expect = 0.031, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 2 SRVYVGNLDSR-VSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAI 55
SR+++GNL + VS+ DL F +G I + + + FI FD+ + +DAI
Sbjct: 11 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAI 62
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 33.5 bits (75), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 34/66 (51%), Gaps = 6/66 (9%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFG-VIRSVWVARR-----PPGYAFIDFDDYRDAQDAI 55
+ +++G+L+ + E + F G + SV + R P GY F++F D A+ +
Sbjct: 10 ASLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEFADLATAEKCL 69
Query: 56 RELDGK 61
+++GK
Sbjct: 70 HKINGK 75
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 33.5 bits (75), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ VYVG LD +VSE L + F G + + + + + GY F++F DA AI+
Sbjct: 16 ATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIK 75
Query: 57 ELD 59
+D
Sbjct: 76 IMD 78
>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 = 33.5 bits (75), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+YVGN+D + +LE F G + V + + P G+A+I+F D + ++
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
>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 = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ +YV NL +++ L+ F +G I + R RP G AF+ ++ +AQ+AI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 57 ELD 59
L+
Sbjct: 74 ALN 76
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ + V + + V E L F +G I SV + R+ GY F+ F AQ AI
Sbjct: 42 LRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAI 101
Query: 56 RELDGKN 62
L+G N
Sbjct: 102 AGLNGFN 108
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 33.1 bits (74), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 11/68 (16%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVI--------RSVWVARRPPGYAFIDFDDYRDAQD 53
+ +YV L +S++++E F +G I ++ V+R G FI FD +A++
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSR---GVGFIRFDKRIEAEE 147
Query: 54 AIRELDGK 61
AI+ L+G+
Sbjct: 148 AIKGLNGQ 155
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 19 EDEFR-VFGVIRSV--------WVARRPPGYAFIDFDDYRDAQDAIRELDG 60
+DEF+ +FG I + + + GY F+++ D DA AI L+G
Sbjct: 18 QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
>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 = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+YVGN+D + +LE F G + V + + P G+A+I+F D + ++
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 33.1 bits (74), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 33/64 (51%), Gaps = 6/64 (9%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
M +YVGNL + +++ F FG + +V + ++P G+ F++ + +AI
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQE-ESVSEAI 59
Query: 56 RELD 59
+LD
Sbjct: 60 AKLD 63
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 2 SRVYVGNLDSR-VSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAI 55
SR+++GNL + VS+ DL F +G I + + + FI FD+ + +DAI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAI 74
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 7/64 (10%)
Query: 13 VSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIRELDGK--NGWR 65
+ERDL + F +G I V + +RR G+AF+ F++ DA++A +G +G R
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 66 VELS 69
+ +S
Sbjct: 87 IRVS 90
>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 = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 12/62 (19%), Positives = 35/62 (56%), Gaps = 4/62 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWV----ARRPPGYAFIDFDDYRDAQDAIREL 58
++++ L ++ +LE+ + G ++ + + A +P G A++++++ A A+ ++
Sbjct: 19 KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKM 78
Query: 59 DG 60
DG
Sbjct: 79 DG 80
>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 = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 32/64 (50%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP-----GYAFIDFDDYRDAQDAIR 56
+ + V L ++R+L FR G I + + R GYAF+DF D+Q AI+
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 57 ELDG 60
L+G
Sbjct: 75 VLNG 78
Score = 32.7 bits (73), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ +YV NL +++ L+ F +G I + R RP G AF+ ++ +AQ+AI
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 57 ELD 59
L+
Sbjct: 161 ALN 163
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 37/70 (52%), Gaps = 7/70 (10%)
Query: 4 VYVGNLDSRVSERDLEDEFRVF--GVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
+YV NL SE +E EF G + V R YAF+ F + DA +A++ L+GK
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD---YAFVHFSNREDAVEAMKALNGK 74
Query: 62 --NGWRVELS 69
+G +E++
Sbjct: 75 VLDGSPIEVT 84
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 2 SRVYVGNLDSR-VSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAI 55
SR+++GNL + VS+ DL F +G I + + + FI FD+ + +DAI
Sbjct: 23 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAI 74
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.1 bits (74), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 4/61 (6%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPPGYAFIDFDDYRDAQDAIRELD 59
V+VGNL++RV E L + F G + V + + +P + F+ F AI L+
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
Query: 60 G 60
G
Sbjct: 79 G 79
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 33.1 bits (74), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 2 SRVYVGNLDSR-VSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAI 55
SR+++GNL + VS+ DL F +G I + + + FI FD+ + +DAI
Sbjct: 3 SRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAI 54
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 32.7 bits (73), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-RPPGYAFIDFDDYRDAQDAI-----RE 57
+ + NL +E L++ F I+ + GYAFI+F + DA++A+ RE
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKRE 77
Query: 58 LDGKNGWRVEL 68
++G+ R+EL
Sbjct: 78 IEGR-AIRLEL 87
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 32.7 bits (73), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 11/67 (16%)
Query: 13 VSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIR-----ELDGKN 62
+ERDL + F +G I V + +RR G+AF+ F++ DA++A ELDG+
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 117
Query: 63 GWRVELS 69
RV+ S
Sbjct: 118 -IRVDFS 123
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 32.7 bits (73), Expect = 0.063, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 32/58 (55%), Gaps = 3/58 (5%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELD 59
++++VGN+ + ++L +F +G + + + YAF+ + DA +AIR LD
Sbjct: 11 TKLHVGNISPTCTNQELRAKFEEYGPVIECDIVK---DYAFVHMERAEDAVEAIRGLD 65
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 32.7 bits (73), Expect = 0.065, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 37/67 (55%), Gaps = 11/67 (16%)
Query: 13 VSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIR-----ELDGKN 62
+ERDL + F +G I V + +RR G+AF+ F++ DA++A ELDG+
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRR 86
Query: 63 GWRVELS 69
RV+ S
Sbjct: 87 -IRVDFS 92
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 32.3 bits (72), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWV----ARRPPGYAFIDFDDYRDAQDAIREL 58
++ V NLD VS+ D+++ F FG ++ V + R G A + F+ DA A+++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQY 89
Query: 59 DG 60
+G
Sbjct: 90 NG 91
>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 = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 21/68 (30%), Positives = 37/68 (54%), Gaps = 11/68 (16%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFG-VIRS-------VWVARRPPGYAFIDFDDYRDAQD 53
+ +YV L +++++LE F +G +I S V+R G FI FD +A++
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSR---GVGFIRFDKRIEAEE 145
Query: 54 AIRELDGK 61
AI+ L+G+
Sbjct: 146 AIKGLNGQ 153
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIR 56
+ + V L +++ + F G I S + R + GY F+++ D +DA+ AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 57 ELDG 60
L+G
Sbjct: 63 TLNG 66
>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
Peptide, Including Two Cchc Zn-Binding Motifs
Length = 37
Score = 32.3 bits (72), Expect = 0.077, Method: Composition-based stats.
Identities = 9/15 (60%), Positives = 12/15 (80%)
Query: 93 CYECGEPGHFARECR 107
CY CG+PGH + +CR
Sbjct: 3 CYNCGKPGHLSSQCR 17
Score = 32.3 bits (72), Expect = 0.079, Method: Composition-based stats.
Identities = 8/15 (53%), Positives = 14/15 (93%)
Query: 93 CYECGEPGHFARECR 107
C++C +PGHF+++CR
Sbjct: 22 CFKCKQPGHFSKQCR 36
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 32.3 bits (72), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 26/74 (35%), Positives = 39/74 (52%), Gaps = 11/74 (14%)
Query: 6 VGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIR---- 56
V L +ERDL + F +G I V + +RR G+AF+ F++ DA++A
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 57 -ELDGKNGWRVELS 69
ELDG+ RV+ S
Sbjct: 77 MELDGRR-IRVDFS 89
>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 = 32.0 bits (71), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 38/81 (46%), Gaps = 13/81 (16%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRS---VWVARRPP--GYAFIDFDDYRDAQDAIRE 57
++VG+L+ V + L + F+ F S +W + GY F+ F DAQ+A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 58 LDGK--NG------WRVELSH 70
+ G+ NG W +L H
Sbjct: 63 MQGQDLNGRPLRINWAAKLEH 83
>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 = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 4/61 (6%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA----RRPPGYAFIDFDDYRDAQDAIRELD 59
+YVGNL +E + + F G I+ + + + G+ F+++ DA++A+R ++
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYIN 80
Query: 60 G 60
G
Sbjct: 81 G 81
>pdb|2A51|A Chain A, Structure Of The (13-51) Domain Of The Nucleocapsid
Protein Ncp8 From Sivlhoest
Length = 39
Score = 32.0 bits (71), Expect = 0.11, Method: Composition-based stats.
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
L C+ CG+PGH AR CR
Sbjct: 1 LTCFNCGKPGHTARMCR 17
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV----ARRPPGYAFIDFDDYRDAQDAIRE 57
+++ V NLD VS+ D+++ F FG ++ V + R G A + F+ DA A+++
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 58 LDG 60
G
Sbjct: 96 YKG 98
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 32.0 bits (71), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV----ARRPPGYAFIDFDDYRDAQDAIRE 57
+++ V NLD VS+ D+++ F FG ++ V + R G A + F+ DA A+++
Sbjct: 36 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 95
Query: 58 LDG 60
G
Sbjct: 96 YKG 98
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/59 (28%), Positives = 32/59 (54%), Gaps = 3/59 (5%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
+++VGN+ + + ++L F G + V + YAF+ + DA+ AI +L+GK
Sbjct: 11 KIFVGNVSAACTSQELRSLFERRGRVIECDVVKD---YAFVHMEKEADAKAAIAQLNGK 66
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.2 bits (69), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 34/75 (45%), Gaps = 6/75 (8%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVW-----VARRPPGYAFIDFDDYRDAQDAIR 56
S +Y+ L +++DL + +G I S + GY F+DFD AQ A+
Sbjct: 6 SGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAVT 65
Query: 57 ELDGKNGWRVELSHN 71
L +G + +++
Sbjct: 66 ALKA-SGVQAQMAKQ 79
>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 = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ +++VG + E L D F +G I + + + + G+AF+ FDD+ D+ D I
Sbjct: 97 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 155
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ +++VG + E L D F +G I + + + + G+AF+ FDD+ D+ D I
Sbjct: 105 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 31.2 bits (69), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ +++VG + E L D F +G I + + + + G+AF+ FDD+ D+ D I
Sbjct: 102 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 160
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ +++VG + E L D F +G I + + + + G+AF+ FDD+ D+ D I
Sbjct: 103 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 161
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ +++VG + E L D F +G I + + + + G+AF+ FDD+ D+ D I
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 162
>pdb|2E5J|A Chain A, Solution Structure Of Rna Binding Domain In
Methenyltetrahydrofolate Synthetase Domain Containing
Length = 97
Score = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 4/59 (6%)
Query: 4 VYVGNL--DSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
VYVGNL D+RVS DL+ R G + + P AF+ + D AQ A+ L G
Sbjct: 22 VYVGNLPRDARVS--DLKRALRELGSVPLRLTWQGPRRRAFLHYPDSAAAQQAVSCLQG 78
>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 = 31.2 bits (69), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 6/60 (10%)
Query: 1 MSRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAI 55
+ +++VG + E L D F +G I + + + + G+AF+ FDD+ D+ D I
Sbjct: 104 VKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDH-DSVDKI 162
>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 = 31.2 bits (69), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 4/62 (6%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWV----ARRPPGYAFIDFDDYRDAQDAIREL 58
++ V NLD VS+ D+++ F FG ++ V + R G A + F+ DA A ++
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQY 90
Query: 59 DG 60
+G
Sbjct: 91 NG 92
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 31.2 bits (69), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
+YVG L V ++ L F FG I + + + G+AF++F+ DA AI +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 59 D 59
+
Sbjct: 126 N 126
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.2 bits (69), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 34/69 (49%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
S+V+VG ++ +L+ F +G + V++ + +AF+ F D + AQ E
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLII 71
Query: 62 NGWRVELSH 70
G V +S+
Sbjct: 72 KGISVHISN 80
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 30.8 bits (68), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 4/63 (6%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWV----ARRPPGYAFIDFDDYRDAQDAIRE 57
+++ V NLD VS+ D+++ F FG ++ V + R G A + F+ DA A+++
Sbjct: 89 AKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQ 148
Query: 58 LDG 60
G
Sbjct: 149 YKG 151
>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 = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA-----RRPPGYAFIDFDDYRDAQDAIREL 58
+YVGNL +E + + F G I+ + + + G+ F+++ DA++A+R +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYI 101
Query: 59 DG 60
+G
Sbjct: 102 NG 103
>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 = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
VY+G++ +E + D G + ++ + R GYAFI+F D + A+R L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 59 DG 60
+G
Sbjct: 67 NG 68
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 30.4 bits (67), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
+YVG L V ++ L F FG I + + + G+AF++F+ DA AI +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 59 D 59
+
Sbjct: 75 N 75
>pdb|1HVN|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|1HVO|E Chain E, Zinc-And Sequence-Dependent Binding To Nucleic Acids By
The N-Terminal Zinc Finger Domain Of The Hiv-1
Nucleocapsid Protein: Nmr Structure Of The Complex With
The Psi-Site Analog, DACGCC
pdb|2ZNF|A Chain A, High-Resolution Structure Of An Hiv Zinc Fingerlike Domain
Via A New Nmr-Based Distance Geometry Approach
Length = 18
Score = 30.4 bits (67), Expect = 0.29, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH AR CR
Sbjct: 1 VKCFNCGKEGHIARNCR 17
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 30.4 bits (67), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
VY+G++ +E + D G + ++ + R GYAFI+F D + A+R L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 59 DG 60
+G
Sbjct: 65 NG 66
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 30.4 bits (67), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 5/62 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
VY+G++ +E + D G + ++ + R GYAFI+F D + A+R L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 59 DG 60
+G
Sbjct: 66 NG 67
>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 = 30.4 bits (67), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
+YVG L V ++ L F FG I + + + G+AF++F+ DA AI +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 59 D 59
+
Sbjct: 70 N 70
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 30.0 bits (66), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
+YVG L V ++ L F FG I + + + G+AF++F+ DA AI +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 59 D 59
+
Sbjct: 68 N 68
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 43/83 (51%), Gaps = 15/83 (18%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIR----------SVWVAR---RPPGYAFIDFDDY 48
S +YV L+ V+ DL D F+ GV++ +++ + +P G A + ++D
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 49 RDAQDAIRELDGKN--GWRVELS 69
A+ A+ DGK+ G ++++S
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVS 98
>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 = 30.0 bits (66), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 30/61 (49%), Gaps = 5/61 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWV-----ARRPPGYAFIDFDDYRDAQDAIREL 58
+YVG L V ++ L F FG I + + + G+AF++F+ DA AI +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 59 D 59
+
Sbjct: 65 N 65
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 29.6 bits (65), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 34/69 (49%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDGK 61
S V+VG ++E +L + F +G + V++ + +AF+ F D + AQ E
Sbjct: 6 SGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLII 65
Query: 62 NGWRVELSH 70
G V +S+
Sbjct: 66 KGISVHISN 74
>pdb|1NCP|N Chain N, Structural Characterization Of A 39 Residue Synthetic
Peptide Containing The Two Zinc Binding Domains From The
Hiv-1 P7 Nucleocapsid Protein By Cd And Nmr Spectroscopy
Length = 17
Score = 29.6 bits (65), Expect = 0.55, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH AR CR
Sbjct: 1 VKCFNCGKEGHTARNCR 17
>pdb|1BJ6|A Chain A, 1h Nmr Of (12-53) Ncp7D(ACGCC) COMPLEX, 10 STRUCTURES
pdb|1ESK|A Chain A, Solution Structure Of Ncp7 From Hiv-1
Length = 42
Score = 29.3 bits (64), Expect = 0.62, Method: Composition-based stats.
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH AR CR
Sbjct: 2 VKCFNCGKEGHTARNCR 18
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 29.3 bits (64), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 9/51 (17%)
Query: 19 EDEFR-VFGVIRSV--------WVARRPPGYAFIDFDDYRDAQDAIRELDG 60
+DEF+ +FG I + + + GY F+++ D DA AI L+G
Sbjct: 18 QDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNG 68
>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 = 28.9 bits (63), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVW-----VARRPPGYAFIDFDDYRDAQDAIR 56
+ + V L +++ +L F G + S VA GY F+++ +DA+ AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 57 ELDG 60
L+G
Sbjct: 65 TLNG 68
>pdb|2L4L|A Chain A, Structural Insights Into The Ctar Dna Recognition By The
Hiv-1 Nucleocapsid Protein: Role Of Sugar Deoxyriboses
In The Binding Polarity Of Nc
Length = 45
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 90 DLKCYECGEPGHFARECR 107
++KC+ CG+ GH AR CR
Sbjct: 2 NVKCFNCGKEGHTARNCR 19
>pdb|2EXF|A Chain A, Solution Structure Of The Hiv-1 Nucleocapsid (Ncp7(12-55))
Complexed With The Dna (-) Primer Binding Site
pdb|2JZW|A Chain A, How The Hiv-1 Nucleocapsid Protein Binds And Destabilises
The (-)primer Binding Site During Reverse Transcription
Length = 44
Score = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 10/18 (55%), Positives = 14/18 (77%)
Query: 90 DLKCYECGEPGHFARECR 107
++KC+ CG+ GH AR CR
Sbjct: 1 NVKCFNCGKEGHTARNCR 18
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDYRDAQDAIREL 58
V+VG+L ++ + F FG I V + + GY F+ F + DA++AI+++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 68
Query: 59 DGK 61
G+
Sbjct: 69 GGQ 71
>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 = 28.5 bits (62), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/63 (22%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 4 VYVGNLDSRVSERDLEDE----FRVFGVIRSVWVAR--RPPGYAFIDFDDYRDAQDAIRE 57
+Y+ N++ ++ + +L+ F FG + + + + G AF+ F + + +A+R+
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQ 68
Query: 58 LDG 60
L G
Sbjct: 69 LQG 71
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 4/58 (6%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVI-RSVWVAR---RPPGYAFIDFDDYRDAQDAI 55
+ + V NL VS LE+ F VFG + R+V + RP G ++F A+ A+
Sbjct: 97 ASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSGKGIVEFSGKPAARKAL 154
>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 = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRP-------------PGYAFIDFDDY 48
+ ++V L V+ + D F+ G+I++ +P G A + FDD
Sbjct: 14 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 73
Query: 49 RDAQDAIRELDGK 61
A+ AI DGK
Sbjct: 74 PSAKAAIDWFDGK 86
>pdb|1AAF|A Chain A, Nucleocapsid Zinc Fingers Detected In Retroviruses: Exafs
Studies On Intact Viruses And The Solution-State
Structure Of The Nucleocapsid Protein From Hiv-1
Length = 55
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH A+ CR
Sbjct: 13 IKCFNCGKEGHIAKNCR 29
>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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 5/64 (7%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVW-----VARRPPGYAFIDFDDYRDAQDAIR 56
+ + V L ++ +L F G + S VA GY F+++ +DA+ AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 57 ELDG 60
L+G
Sbjct: 80 TLNG 83
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 29/64 (45%), Gaps = 4/64 (6%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYA----FIDFDDYRDAQDAIRE 57
+ +Y+ NL + E++LE+ + FG + S + R G + F + + I
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 58 LDGK 61
+GK
Sbjct: 86 FNGK 89
>pdb|1NC8|A Chain A, High-Resolution Solution Nmr Structure Of The Minimal
Active Domain Of The Human Immunodeficiency Virus Type-2
Nucleocapsid Protein, 15 Structures
Length = 29
Score = 28.1 bits (61), Expect = 1.6, Method: Composition-based stats.
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 91 LKCYECGEPGHFARECR 107
++C+ CG+ GH AR+CR
Sbjct: 7 IRCWNCGKEGHSARQCR 23
>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 = 28.1 bits (61), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPP-----GYAFIDFDDYRDAQDAIRE 57
+ +VG L S++DL+D F FG + + P G+ FI F +DA +
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKV 69
Query: 58 LDGK 61
LD K
Sbjct: 70 LDQK 73
>pdb|2M3Z|A Chain A, Nmr Solution Structure Of Hiv-1 Nucleocapsid Protein In
Complex With An Inhibitor Displaying A 2 Inhibitors:1 Nc
Stoichiometry
Length = 55
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH A+ CR
Sbjct: 13 VKCFNCGKEGHIAKNCR 29
>pdb|1F6U|A Chain A, Nmr Structure Of The Hiv-1 Nucleocapsid Protein Bound To
Stem-Loop Sl2 Of The Psi-Rna Packaging Signal.
Implications For Genome Recognition
Length = 56
Score = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH A+ CR
Sbjct: 13 VKCFNCGKEGHIAKNCR 29
>pdb|2DI2|A Chain A, Nmr Structure Of The Hiv-2 Nucleocapsid Protein
Length = 29
Score = 27.7 bits (60), Expect = 1.8, Method: Composition-based stats.
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 91 LKCYECGEPGHFARECR 107
++C+ CG+ GH AR+CR
Sbjct: 7 IRCWACGKEGHSARQCR 23
>pdb|1A1T|A Chain A, Structure Of The Hiv-1 Nucleocapsid Protein Bound To The
Sl3 Psi-Rna Recognition Element, Nmr, 25 Structures
pdb|1MFS|A Chain A, Dynamical Behavior Of The Hiv-1 Nucleocapsid Protein; Nmr,
30 Structures
Length = 55
Score = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 91 LKCYECGEPGHFARECR 107
+KC+ CG+ GH A+ CR
Sbjct: 13 VKCFNCGKEGHIAKNCR 29
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 27.7 bits (60), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%), Gaps = 5/52 (9%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR-----RPPGYAFIDFDDY 48
S + V L + +E+DL++ F FG + V V + G+ F+ F +Y
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEY 67
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRP-------------PGYAFIDFDDY 48
+ ++V L V+ + D F+ G+I++ +P G A + FDD
Sbjct: 8 NTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDP 67
Query: 49 RDAQDAIRELDGK 61
A+ AI DGK
Sbjct: 68 PSAKAAIDWFDGK 80
>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 = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 10/66 (15%)
Query: 3 RVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPP---GYAFIDFDDYR---DAQ 52
+++VG + SE+DL + F +G + + V R PP G F+ F + +AQ
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 53 DAIREL 58
+A+ +
Sbjct: 65 NALHNM 70
>pdb|2EC7|A Chain A, Solution Structure Of Human Immunodificiency Virus Type-2
Nucleocapsid Protein
Length = 49
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 9/17 (52%), Positives = 14/17 (82%)
Query: 91 LKCYECGEPGHFARECR 107
++C+ CG+ GH AR+CR
Sbjct: 7 IRCWNCGKEGHSARQCR 23
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 27.3 bits (59), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 8 NLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
NL +V++ +L++ F IR V + G A+I+F DA+ E G
Sbjct: 100 NLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQG 152
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 17 DLEDEFRVFGVIRSVWV-ARRPPGYAFIDFDDYRDAQDAIRELDGK 61
DL E FG IR + + R P G A + F D +A I+ LDG+
Sbjct: 42 DLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGR 87
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 31/61 (50%), Gaps = 3/61 (4%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVARRPPG---YAFIDFDDYRDAQDAIRELDG 60
+YVGNL V+E + F G +S + Y F++F ++RDA A+ ++G
Sbjct: 18 LYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDPYCFVEFYEHRDAAAALAAMNG 77
Query: 61 K 61
+
Sbjct: 78 R 78
>pdb|2YSA|A Chain A, Solution Structure Of The Zinc Finger Cchc Domain From The
Human Retinoblastoma-Binding Protein 6 (Retinoblastoma-
Binding Q Protein 1, Rbq-1)
Length = 55
Score = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 93 CYECGEPGHFAREC 106
C+ CG+PGH+ + C
Sbjct: 10 CFRCGKPGHYIKNC 23
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 2 SRVYVGNLDSRVSERDLEDEFRVFGVIRSVWVAR----RPPGYAFIDFDDYRDAQDAIRE 57
S V+V NLD +V + L++ F + GV+ + + G + F+ +A AI
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 58 LDGK 61
+G+
Sbjct: 76 FNGQ 79
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 8 NLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
NL ++E +L++ F IR V + G A+I+F DA+ + E G
Sbjct: 23 NLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 75
>pdb|2IHX|A Chain A, Solution Structure Of The Rous Sarcoma Virus Nucleocapsid
Protein:upsi Rna Packaging Signal Complex
Length = 61
Score = 26.9 bits (58), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 93 CYECGEPGHFAREC 106
CY CG PGH+ +C
Sbjct: 7 CYTCGSPGHYQAQC 20
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V ++ E +++++F +G I+++ + RR GYA ++++ ++ A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 59 DG 60
+G
Sbjct: 89 NG 90
>pdb|3QN3|A Chain A, Phosphopyruvate Hydratase From Campylobacter Jejuni.
pdb|3QN3|B Chain B, Phosphopyruvate Hydratase From Campylobacter Jejuni.
pdb|3QN3|C Chain C, Phosphopyruvate Hydratase From Campylobacter Jejuni.
pdb|3QN3|D Chain D, Phosphopyruvate Hydratase From Campylobacter Jejuni
Length = 417
Score = 26.6 bits (57), Expect = 4.5, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 16 RDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQ--DAIRELDGKNGW 64
RD ++ F GV+++V + D + Q D +RELDG N +
Sbjct: 55 RDNDERFGGKGVLKAVANVNETIADEILGLDAFNQTQLDDTLRELDGTNNY 105
>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 = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 26/53 (49%)
Query: 8 NLDSRVSERDLEDEFRVFGVIRSVWVARRPPGYAFIDFDDYRDAQDAIRELDG 60
NL ++E +L++ F IR V + G A+I+F DA+ + E G
Sbjct: 106 NLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQG 158
>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger 1)
Length = 21
Score = 26.2 bits (56), Expect = 5.4, Method: Composition-based stats.
Identities = 7/15 (46%), Positives = 11/15 (73%)
Query: 93 CYECGEPGHFARECR 107
C+ CG+ GH R+C+
Sbjct: 5 CFSCGKTGHIKRDCK 19
>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 = 25.8 bits (55), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 14/62 (22%), Positives = 35/62 (56%), Gaps = 5/62 (8%)
Query: 4 VYVGNLDSRVSERDLEDEFRVFGVIRSVWVA--RRP---PGYAFIDFDDYRDAQDAIREL 58
++V ++ E +++++F +G I+++ + RR GYA ++++ ++ A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 59 DG 60
+G
Sbjct: 135 NG 136
>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
Length = 60
Score = 25.8 bits (55), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 8/15 (53%), Positives = 12/15 (80%)
Query: 93 CYECGEPGHFARECR 107
C++CG+ GHFA+ C
Sbjct: 4 CFKCGKKGHFAKNCH 18
>pdb|1Q3Y|A Chain A, Nmr Structure Of The Cys28his Mutant (D Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1.
pdb|1Q3Z|A Chain A, Nmr Structure Of The Cys28his Mutant (e Form) Of The
Nucleocapsid Protein Ncp7 Of Hiv-1
Length = 42
Score = 25.4 bits (54), Expect = 8.8, Method: Composition-based stats.
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 90 DLKCYECGEPGHFARECR 107
++KC+ CG+ GH AR R
Sbjct: 1 NVKCFNCGKEGHTARNHR 18
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
0.324 0.143 0.463
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,057,184
Number of Sequences: 62578
Number of extensions: 101339
Number of successful extensions: 478
Number of sequences better than 100.0: 173
Number of HSP's better than 100.0 without gapping: 101
Number of HSP's successfully gapped in prelim test: 72
Number of HSP's that attempted gapping in prelim test: 311
Number of HSP's gapped (non-prelim): 202
length of query: 131
length of database: 14,973,337
effective HSP length: 88
effective length of query: 43
effective length of database: 9,466,473
effective search space: 407058339
effective search space used: 407058339
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 46 (22.3 bits)