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= 024366
(268 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 58.5 bits (140), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 36/79 (45%), Positives = 47/79 (59%), Gaps = 7/79 (8%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRGLDNI 59
I+VGN + R ++E +F KYG I +D+K+ FAFV FED RDA DA+ G D
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDG- 83
Query: 60 PFGYDRRRLSVEWARGERG 78
+ YD RL VE+ R RG
Sbjct: 84 -YDYDGYRLRVEFPRSGRG 101
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 6/59 (10%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRRN---FAFVQFETQEEATKALESTD 149
++V N P R +DI+ F YG + + ++ RR FAFV+FE +A A+ D
Sbjct: 25 IYVGNLPP-DIRTKDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRD 82
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 43/78 (55%), Gaps = 10/78 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
I V N +TR+++L+ LF +G I R+ + GFAF+ F DAA AI G+
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 57 DNIPFGYDRRRLSVEWAR 74
FGYD L+VEWA+
Sbjct: 78 SG--FGYDHLILNVEWAK 93
Score = 35.0 bits (79), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 35/66 (53%), Gaps = 8/66 (12%)
Query: 106 TRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTDRSKLVDRV 157
TRE D++ F P+G++ + + ++ FAF+ F +E+A +A+ +
Sbjct: 27 TRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYDHLI 86
Query: 158 ISVEYA 163
++VE+A
Sbjct: 87 LNVEWA 92
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 53.9 bits (128), Expect = 9e-08, Method: Compositional matrix adjust.
Identities = 29/57 (50%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK---SGFAFVYFEDDRDAADAIRGLDN 58
++VGN + ELER FS YG + V + GFAFV FED RDA DA+RGLD
Sbjct: 3 VYVGNLGTGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDG 59
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 110 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYALKD 166
+++R F YG + V I RN FAFV+FE +A A+ D + + VE L
Sbjct: 16 ELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVE--LST 73
Query: 167 DSERDDRYDSP 177
R R+D P
Sbjct: 74 GMPRRSRFDRP 84
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMK---SGFAFVYFEDDRDAADAIRGLD 57
+ ++VGN ++ELER F YG + V + GFAFV FED RDAADA+R LD
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLD 131
Query: 58 NIPFGYDRRRLSVEWARGER 77
R R VE + GE+
Sbjct: 132 GRTLCGCRVR--VELSNGEK 149
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 110 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
+++R F YG + V + RN FAFV+FE +A A+ D L + VE +
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVELS 145
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/80 (42%), Positives = 44/80 (55%), Gaps = 5/80 (6%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMK---SGFAFVYFEDDRDAADAIRGLD 57
+ ++VGN ++ELER F YG + V + GFAFV FED RDAADA+R LD
Sbjct: 72 LDCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELD 131
Query: 58 NIPFGYDRRRLSVEWARGER 77
R R VE + GE+
Sbjct: 132 GRTLCGCRVR--VELSNGEK 149
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 110 DIKRHFEPYGNVLHVRIRRN---FAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
+++R F YG + V + RN FAFV+FE +A A+ D L + VE +
Sbjct: 89 ELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELS 145
>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 = 51.2 bits (121), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 77/171 (45%), Gaps = 28/171 (16%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERV----DMKS----GFAFVYFEDDRDAADAIRGL 56
++VG+ + ++ L FS G I + DM + G+A+V F+ ADA R L
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ---PADAERAL 74
Query: 57 DNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF 115
D + F + + + + W++ + + G +F+ N D + + F
Sbjct: 75 DTMNFDVIKGKPVRIMWSQRDPSLRKSG---------VGNIFIKNLDK-SIDNKALYDTF 124
Query: 116 EPYGNVLHVRI------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV 160
+GN+L ++ + + FV FETQE A +A+E + L DR + V
Sbjct: 125 SAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 36/73 (49%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNIPF 61
S + VGN EL F +YG + D+ +AFV+ E DA +AIRGLDN F
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDNTEF 69
Query: 62 GYDRRRLSVEWAR 74
R + + +R
Sbjct: 70 QGKRMHVQLSTSR 82
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 39/73 (53%), Gaps = 1/73 (1%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 150
+ + L V N P T + +++ FE YG V+ I +++AFV E E+A +A+ D
Sbjct: 8 KASTKLHVGNISPTCTNQ-ELRAKFEEYGPVIECDIVKDYAFVHMERAEDAVEAIRGLDN 66
Query: 151 SKLVDRVISVEYA 163
++ + + V+ +
Sbjct: 67 TEFQGKRMHVQLS 79
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 43/171 (25%), Positives = 77/171 (45%), Gaps = 28/171 (16%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERV----DMKS----GFAFVYFEDDRDAADAIRGL 56
++VG+ + ++ L FS G I + DM + G+A+V F+ ADA R L
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQ---PADAERAL 69
Query: 57 DNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF 115
D + F + + + + W++ + + G +F+ N D + + F
Sbjct: 70 DTMNFDVIKGKPVRIMWSQRDPSLRKSG---------VGNIFIKNLDK-SIDNKALYDTF 119
Query: 116 EPYGNVLHVRI------RRNFAFVQFETQEEATKALESTDRSKLVDRVISV 160
+GN+L ++ + + FV FETQE A +A+E + L DR + V
Sbjct: 120 SAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/58 (37%), Positives = 37/58 (63%), Gaps = 1/58 (1%)
Query: 1 MSRPIFVGNFE-YETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLD 57
M+ +F+GN ++S++E +FSKYG+I + GFAFV + ++R+A A+ G D
Sbjct: 14 MNSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGED 71
Score = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 155
+F+ N + + ++ D++ F YG ++ + + FAFVQ+ + A A+ D +
Sbjct: 18 VFIGNLNTLVVKKSDVEAIFSKYGKIVGCSVHKGFAFVQYVNERNARAAVAGEDGRMIAG 77
Query: 156 RVISVEYA 163
+V+ + A
Sbjct: 78 QVLDINLA 85
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 48.5 bits (114), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 20/52 (38%), Positives = 30/52 (57%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGL 56
+F+GN E + E+ LF +YG++ D+ + FV+ ED A DAIR L
Sbjct: 11 LFIGNLPREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNL 62
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 155
LF+ N P E++I+ FE YG VL I +N+ FV E + A A+ + KL
Sbjct: 11 LFIGNL-PREATEQEIRSLFEQYGKVLECDIIKNYGFVHIEDKTAAEDAIRNLHHYKLHG 69
Query: 156 RVISVE 161
I+VE
Sbjct: 70 VNINVE 75
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 48.1 bits (113), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 31/90 (34%), Positives = 48/90 (53%), Gaps = 11/90 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIRGL 56
+FVG ++T + LE++FSKYG+I V + GF FV FE+ DA DA+ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 57 DNIPFGYDRRRLSVEWARGERGRHRDGSKS 86
+ D R++ V+ A G+ +R G S
Sbjct: 75 NGKS--VDGRQIRVDQA-GKSSDNRSGPSS 101
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 40/85 (47%), Gaps = 13/85 (15%)
Query: 96 LFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
LFV ++FD T E+ +++ F YG + V + R F FV FE ++A A+
Sbjct: 15 LFVGGLSFD---TNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM 71
Query: 146 ESTDRSKLVDRVISVEYALKDDSER 170
+ + + R I V+ A K R
Sbjct: 72 MAMNGKSVDGRQIRVDQAGKSSDNR 96
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 30/90 (33%), Positives = 46/90 (51%), Gaps = 6/90 (6%)
Query: 74 RGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFV 133
RG HR + ++N R LFV F P+ +E ++ F P+G + V+I FAFV
Sbjct: 17 RGSHMHHRQEGE-LSNTR----LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFV 70
Query: 134 QFETQEEATKALESTDRSKLVDRVISVEYA 163
+FE E A KA+E ++ + V Y+
Sbjct: 71 EFEEAESAAKAIEEVHGKSFANQPLEVVYS 100
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAI 53
+FV F + ++SEL +F +G ++ V + +GFAFV FE+ AA AI
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAI 82
>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 = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 38/78 (48%), Gaps = 10/78 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
+ V N Y T L R+F KYGR+ V + GFAFV F D RDA DA+ +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 57 DNIPFGYDRRRLSVEWAR 74
D D R L V+ AR
Sbjct: 110 DGAVL--DGRELRVQMAR 125
Score = 35.8 bits (81), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 30/99 (30%), Positives = 47/99 (47%), Gaps = 13/99 (13%)
Query: 78 GRHRDGSKSMANQRP---TKTLFVINFDPI--RTRERDIKRHFEPYGNVLHVRI------ 126
G + G SM+ RP + + + D + RT ++R FE YG V V I
Sbjct: 26 GGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYT 85
Query: 127 --RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
R FAFV+F + +A A+++ D + L R + V+ A
Sbjct: 86 KESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 124
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 33/52 (63%), Gaps = 1/52 (1%)
Query: 5 IFVGNFEYE-TRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRG 55
+F+GN ++S++E +FSKYGR+ + G+AFV + ++R A A+ G
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLG 81
Score = 36.2 bits (82), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 15/68 (22%), Positives = 32/68 (47%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 155
+F+ N + ++ D++ F YG V + + +AFVQ+ + A A+ + L
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVHKGYAFVQYSNERHARAAVLGENGRVLAG 89
Query: 156 RVISVEYA 163
+ + + A
Sbjct: 90 QTLDINMA 97
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 45.4 bits (106), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 37/76 (48%), Gaps = 10/76 (13%)
Query: 7 VGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGLDN 58
V N Y T L R+F KYGR+ V + GFAFV F D RDA DA+ +D
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 59 IPFGYDRRRLSVEWAR 74
D R L V+ AR
Sbjct: 135 AVL--DGRELRVQMAR 148
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 8/67 (11%)
Query: 105 RTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDR 156
RT ++R FE YG V V I R FAFV+F + +A A+++ D + L R
Sbjct: 81 RTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGR 140
Query: 157 VISVEYA 163
+ V+ A
Sbjct: 141 ELRVQMA 147
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 44.7 bits (104), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/68 (35%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDRSKLVD 155
LFV F P+ +E ++ F P+G + V+I FAFV+FE E A KA+E +
Sbjct: 7 LFVRPF-PLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAIEEVHGKSFAN 65
Query: 156 RVISVEYA 163
+ + V Y+
Sbjct: 66 QPLEVVYS 73
Score = 42.0 bits (97), Expect = 3e-04, Method: Composition-based stats.
Identities = 20/49 (40%), Positives = 31/49 (63%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAI 53
+FV F + ++SEL +F +G ++ V + +GFAFV FE+ AA AI
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKILNGFAFVEFEEAESAAKAI 55
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 40/79 (50%), Gaps = 4/79 (5%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNIPFGYD 64
IFVGN EL LF + GR+ D+ +AFV+ E + DA AI L+
Sbjct: 12 IFVGNVSAACTSQELRSLFERRGRVIECDVVKDYAFVHMEKEADAKAAIAQLNGKEV--K 69
Query: 65 RRRLSVEWARGERGRHRDG 83
+R++VE + +G+ + G
Sbjct: 70 GKRINVELST--KGQKKSG 86
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 35/76 (46%), Gaps = 10/76 (13%)
Query: 7 VGNFEYETRQSELERLFSKYGRIERV--------DMKSGFAFVYFEDDRDAADAIRGLDN 58
V N Y T L R+F KYGR+ V GFAFV F D RDA DA +D
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 59 IPFGYDRRRLSVEWAR 74
D R L V+ AR
Sbjct: 78 AEL--DGRELRVQVAR 91
Score = 33.5 bits (75), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 37/77 (48%), Gaps = 9/77 (11%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNV--------LHVRIRRNFAFVQFETQEEATKALE 146
TL V N RT ++R FE YG V H + R FAFV+F + +A A
Sbjct: 15 TLKVDNL-TYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 147 STDRSKLVDRVISVEYA 163
+ D ++L R + V+ A
Sbjct: 74 AMDGAELDGRELRVQVA 90
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 31/61 (50%)
Query: 87 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 146
M N P LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 4 MHNIPPKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 63
Query: 147 S 147
Sbjct: 64 C 64
Score = 41.6 bits (96), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 5 IFVGNFEYETRQSE-LERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAI 53
+F+GN + E L R+FS YG I ++++K+ F F+ F++ + DAI
Sbjct: 13 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 62
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 41.6 bits (96), Expect = 4e-04, Method: Composition-based stats.
Identities = 17/55 (30%), Positives = 29/55 (52%)
Query: 92 PTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 146
P LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 1 PKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 55
Score = 38.9 bits (89), Expect = 0.003, Method: Composition-based stats.
Identities = 18/50 (36%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 5 IFVGNFEYETRQSE-LERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAI 53
+F+GN + E L R+FS YG I ++++K+ F F+ F++ + DAI
Sbjct: 5 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 54
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 8/89 (8%)
Query: 83 GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQ 134
GS + TK + + ++ + F P+G++ ++I R FAFV+
Sbjct: 1 GSSGSSGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVE 60
Query: 135 FETQEEATKALESTDRSKLVDRVISVEYA 163
FE E+A A+++ + S+L R I V A
Sbjct: 61 FELAEDAAAAIDNMNESELFGRTIRVNLA 89
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIR 54
R ++VG E L F +G I + + GFAFV FE DAA AI
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 55 GLD 57
++
Sbjct: 73 NMN 75
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 37/81 (45%), Gaps = 10/81 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKS---------GFAFVYFEDDRDAADAIRG 55
I V N ++ Q E+ LFS +G ++ V + GF FV F +DA A
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
L + Y RRL +EWA E
Sbjct: 78 LCHSTHLYG-RRLVLEWADSE 97
Score = 36.2 bits (82), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 46/98 (46%), Gaps = 13/98 (13%)
Query: 82 DGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI---------RRNFAF 132
GS ++ T + ++ P + +R+I+ F +G + VR+ R F F
Sbjct: 3 SGSSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGF 62
Query: 133 VQFETQEEATKALESTDRSK-LVDRVISVEYALKDDSE 169
V F T+++A KA + S L R + +E+A DSE
Sbjct: 63 VDFITKQDAKKAFNALCHSTHLYGRRLVLEWA---DSE 97
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 1 MSRPIFVGNFEYETRQSE-LERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAI 53
M +F+GN + E L R+FS YG I ++++K+ F F+ F++ + DAI
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 74
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTDR 150
LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E +
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIECESQ 79
>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 = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
+FV Y+T +S+L R F YG I+R+ M G+AF+ +E +RD A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 57 DNIPFGYDRRRLSVEWARG 75
D D RR+ V+ RG
Sbjct: 165 DGK--KIDGRRVLVDVERG 181
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 94 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 143
KTLFV +N+D T E ++R FE YG + + + R +AF+++E + +
Sbjct: 103 KTLFVARVNYD---TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 144 ALESTDRSKLVDRVISVE 161
A + D K+ R + V+
Sbjct: 160 AYKHADGKKIDGRRVLVD 177
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 1 MSRPIFVGNFEYETRQSE-LERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAI 53
M +F+GN + E L R+FS YG I ++++K+ F F+ F++ + DAI
Sbjct: 21 MKSRLFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAI 74
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 28/51 (54%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALE 146
LF+ N + D+ R F PYG+++ + I+ F F+QF+ + A+E
Sbjct: 25 LFIGNLPLKNVSKEDLFRIFSPYGHIMQINIKNAFGFIQFDNPQSVRDAIE 75
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/83 (28%), Positives = 43/83 (51%), Gaps = 10/83 (12%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHV-RIRRN--------FAFVQFETQEEATKALE 146
+F+ N DP E+ + F +G +L +I R+ +AF+ F + + + A+E
Sbjct: 8 IFIGNLDP-EIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
Query: 147 STDRSKLVDRVISVEYALKDDSE 169
+ + L +R I+V YA K DS+
Sbjct: 67 AMNGQYLCNRPITVSYAFKKDSK 89
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 41.2 bits (95), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
++V N + ++L R+FSKYG++ +V + G AF+ F D A + R +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 57 DN 58
+N
Sbjct: 79 NN 80
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 37/82 (45%), Gaps = 10/82 (12%)
Query: 92 PTK-TLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEAT 142
P+K T++V N P D+ R F YG V+ V I ++ AF+ F ++ A
Sbjct: 14 PSKSTVYVSNL-PFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQ 72
Query: 143 KALESTDRSKLVDRVISVEYAL 164
+ + +L RVI A+
Sbjct: 73 NCTRAINNKQLFGRVIKASIAI 94
>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 = 40.8 bits (94), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
+FV Y+T +S+L R F YG I+R+ M G+AF+ +E +RD A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 57 DNIPFGYDRRRLSVEWARG 75
D D RR+ V+ RG
Sbjct: 165 DGKKI--DGRRVLVDVERG 181
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 40/78 (51%), Gaps = 13/78 (16%)
Query: 94 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 143
KTLFV +N+D T E ++R FE YG + + + R +AF+++E + +
Sbjct: 103 KTLFVARVNYD---TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHS 159
Query: 144 ALESTDRSKLVDRVISVE 161
A + D K+ R + V+
Sbjct: 160 AYKHADGKKIDGRRVLVD 177
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
+ IFVG + +T + L F +YG+IE +++ K GFAFV F DD D+ D I
Sbjct: 106 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKI 163
Score = 36.2 bits (82), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 29/161 (18%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFE--DDRDAADA 52
R +F+G +ET L F ++G + + V M+ GF FV + ++ DAA
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
R P D R + +R R+ S+ K +FV T E ++
Sbjct: 75 AR-----PHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIFVGGIKE-DTEEHHLR 123
Query: 113 RHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
+FE YG + + I +R FAFV F+ + K +
Sbjct: 124 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
+ IFVG + +T + L F +YG+IE +++ K GFAFV F DD D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKI 162
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 29/161 (18%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFE--DDRDAADA 52
R +F+G +ET L F ++G + + V M+ GF FV + ++ DAA
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
R P D R + +R R+ S+ K +FV T E ++
Sbjct: 74 AR-----PHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIFVGGIKE-DTEEHHLR 122
Query: 113 RHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
+FE YG + + I +R FAFV F+ + K +
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
+ IFVG + +T + L F +YG+IE +++ K GFAFV F DD D+ D I
Sbjct: 104 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKI 161
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 29/161 (18%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFE--DDRDAADA 52
R +F+G +ET L F ++G + + V M+ GF FV + ++ DAA
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
R P D R + +R R+ S+ K +FV T E ++
Sbjct: 73 AR-----PHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIFVGGIKE-DTEEHHLR 121
Query: 113 RHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
+FE YG + + I +R FAFV F+ + K +
Sbjct: 122 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
+ IFVG + +T + L F +YG+IE +++ K GFAFV F DD D+ D I
Sbjct: 105 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKI 162
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 29/161 (18%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFE--DDRDAADA 52
R +F+G +ET L F ++G + + V M+ GF FV + ++ DAA
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
R P D R + +R R+ S+ K +FV T E ++
Sbjct: 74 AR-----PHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIFVGGIKE-DTEEHHLR 122
Query: 113 RHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
+FE YG + + I +R FAFV F+ + K +
Sbjct: 123 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>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 = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
+ IFVG + +T + L F +YG+IE +++ K GFAFV F DD D+ D I
Sbjct: 98 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKI 155
Score = 35.8 bits (81), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 29/161 (18%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFE--DDRDAADA 52
R +F+G +ET L F ++G + + V M+ GF FV + ++ DAA
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
R P D R + +R R+ S+ K +FV T E ++
Sbjct: 67 AR-----PHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIFVGGIKE-DTEEHHLR 115
Query: 113 RHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
+FE YG + + I +R FAFV F+ + K +
Sbjct: 116 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 33/59 (55%), Gaps = 9/59 (15%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
+ IFVG + +T + L F +YG+IE +++ K GFAFV F DD D+ D I
Sbjct: 103 KKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF-DDHDSVDKI 160
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 41/161 (25%), Positives = 66/161 (40%), Gaps = 29/161 (18%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFE--DDRDAADA 52
R +F+G +ET L F ++G + + V M+ GF FV + ++ DAA
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
R P D R + +R R+ S+ K +FV T E ++
Sbjct: 72 AR-----PHKVDGRVV-----EPKRAVSREDSQRPGAHLTVKKIFVGGIKE-DTEEHHLR 120
Query: 113 RHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKAL 145
+FE YG + + I +R FAFV F+ + K +
Sbjct: 121 DYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 40.8 bits (94), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 46/97 (47%), Gaps = 15/97 (15%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
S ++VGN + T + ++ LFSK G I+++ M GF FV + DA +A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 54 RGLDNIPFGYDRRRLSVEWARG-----ERGRHRDGSK 85
R ++ D R + +W G + GR R G +
Sbjct: 99 RYINGTRL--DDRIIRTDWDAGFKEGRQYGRGRSGGQ 133
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/80 (22%), Positives = 37/80 (46%), Gaps = 9/80 (11%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHV--------RIRRNFAFVQFETQEEAT 142
+ + TL+V N T E I F G++ + + F FV++ ++ +A
Sbjct: 37 KKSCTLYVGNL-SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 143 KALESTDRSKLVDRVISVEY 162
A+ + ++L DR+I ++
Sbjct: 96 NAMRYINGTRLDDRIIRTDW 115
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 51/109 (46%), Gaps = 8/109 (7%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
++R +++ N Y+ E+ +F KYG I ++ + + G A+V +ED DA +A+
Sbjct: 7 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDH 66
Query: 56 LDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ-RPTKTLFVINFDP 103
L F R L V + R + +K Q + K + IN DP
Sbjct: 67 LSG--FNVSNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 113
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/91 (29%), Positives = 46/91 (50%), Gaps = 4/91 (4%)
Query: 83 GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEAT 142
GS MA K LFV N T E +++ F +G + V+ +++AF+ F+ ++ A
Sbjct: 4 GSSGMAK---VKVLFVRNLANTVTEEI-LEKAFSQFGKLERVKKLKDYAFIHFDERDGAV 59
Query: 143 KALESTDRSKLVDRVISVEYALKDDSERDDR 173
KA+E + L I + +A D +R +R
Sbjct: 60 KAMEEMNGKDLEGENIEIVFAKPPDQKRKER 90
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/48 (37%), Positives = 30/48 (62%), Gaps = 1/48 (2%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAA 50
+ +FV N + LE+ FS++G++ERV +AF++F D+RD A
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVKKLKDYAFIHF-DERDGA 58
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 40.0 bits (92), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 28/85 (32%), Positives = 41/85 (48%), Gaps = 9/85 (10%)
Query: 88 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 139
AN P L V + T ERD++ F YG + V I R FAFV FE +
Sbjct: 41 ANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVD 99
Query: 140 EATKALESTDRSKLVDRVISVEYAL 164
+A +A E + +L R I V++++
Sbjct: 100 DAKEAKERANGMELDGRRIRVDFSI 124
Score = 34.7 bits (78), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 10/72 (13%)
Query: 14 TRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGLDNIPFGYDR 65
T + +L +FSKYG I V + GFAFVYFE+ DA +A + + D
Sbjct: 58 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DG 115
Query: 66 RRLSVEWARGER 77
RR+ V+++ +R
Sbjct: 116 RRIRVDFSITKR 127
>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 = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/81 (29%), Positives = 40/81 (49%), Gaps = 9/81 (11%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDM-------KSGFAFVYFEDDRDAADAIR 54
S ++VGN + T + ++ LFSK G I+++ M GF FV + DA +A+R
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 55 GLDNIPFGYDRRRLSVEWARG 75
++ D R + +W G
Sbjct: 78 YINGTRL--DDRIIRTDWDAG 96
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 34/60 (56%), Gaps = 7/60 (11%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM------KS-GFAFVYFEDDRDAADAIRGLD 57
+F+G ET + L+ +F K+G I V + KS GFAF+ FE+ DA +A + ++
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Score = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 30/67 (44%), Gaps = 7/67 (10%)
Query: 106 TRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVDRVI 158
T E+ +K F +G + V + R FAF+ FE +A A + + L + I
Sbjct: 19 TNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAI 78
Query: 159 SVEYALK 165
VE A K
Sbjct: 79 KVEQAKK 85
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 35/57 (61%), Gaps = 3/57 (5%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNI 59
+ +FV N + LE+ FS++G++ERV +AFV+FE DR A A++ +D +
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVKKLKDYAFVHFE-DRGA--AVKAMDEM 69
Score = 33.9 bits (76), Expect = 0.098, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFAFVQFETQEEATKALESTD 149
K LFV N T E +++ F +G + V+ +++AFV FE + A KA++ +
Sbjct: 15 VKVLFVRNLATTVTEEI-LEKSFSEFGKLERVKKLKDYAFVHFEDRGAAVKAMDEMN 70
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 84 SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQF 135
S + AN P L V + T ERD++ F YG + V I R FAFV F
Sbjct: 6 SGNRANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 136 ETQEEATKALESTDRSKLVDRVISVEYAL 164
E ++A +A E + +L R I V++++
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRVDFSI 93
Score = 34.7 bits (78), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 10/72 (13%)
Query: 14 TRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGLDNIPFGYDR 65
T + +L +FSKYG I V + GFAFVYFE+ DA +A + + D
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DG 84
Query: 66 RRLSVEWARGER 77
RR+ V+++ +R
Sbjct: 85 RRIRVDFSITKR 96
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 86 SMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFET 137
S AN P L V + T ERD++ F YG + V I R FAFV FE
Sbjct: 5 SRANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFEN 63
Query: 138 QEEATKALESTDRSKLVDRVISVEYAL 164
++A +A E + +L R I V++++
Sbjct: 64 VDDAKEAKERANGMELDGRRIRVDFSI 90
Score = 34.7 bits (78), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 38/72 (52%), Gaps = 10/72 (13%)
Query: 14 TRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGLDNIPFGYDR 65
T + +L +FSKYG I V + GFAFVYFE+ DA +A + + D
Sbjct: 24 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMEL--DG 81
Query: 66 RRLSVEWARGER 77
RR+ V+++ +R
Sbjct: 82 RRIRVDFSITKR 93
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 9/67 (13%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIR 54
R I+VGN Y +++ LFS++G++ V + GF FV +++ ++AI
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEE-SVSEAIA 60
Query: 55 GLDNIPF 61
LDN F
Sbjct: 61 KLDNTDF 67
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 50/109 (45%), Gaps = 8/109 (7%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
++R +++ N Y+ E+ +F KYG I ++ + + G A+V +ED DA +A
Sbjct: 17 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 76
Query: 56 LDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ-RPTKTLFVINFDP 103
L F R L V + R + +K Q + K + IN DP
Sbjct: 77 LSG--FNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 123
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 36/165 (21%), Positives = 72/165 (43%), Gaps = 20/165 (12%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADA 52
MSR ++VG+ YE + + + F+ +G I+ +DM GFAFV +E A A
Sbjct: 28 MSR-VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLA 86
Query: 53 IRGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIK 112
+ ++++ G ++ G+ D + R ++V + + DIK
Sbjct: 87 LEQMNSVMLGGRNIKVGRPSNIGQAQPIID--QLAEEARAFNRIYVASVHQ-DLSDDDIK 143
Query: 113 RHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKALESTD 149
FE +G + + R+ + F+++E + + A+ S +
Sbjct: 144 SVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 188
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 108 ERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVIS 159
E I++ F P+G + + + + FAFV++E E A ALE + L R I
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 101
Query: 160 V 160
V
Sbjct: 102 V 102
>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 = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 115 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 28 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 84
Score = 28.5 bits (62), Expect = 3.7, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIR 54
R ++VG E L F +G I + + GFAFV FE DAA AI
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 55 GLD 57
++
Sbjct: 68 NMN 70
>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 = 38.5 bits (88), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 7/71 (9%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 149
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E +
Sbjct: 8 IFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMN 66
Query: 150 RSKLVDRVISV 160
L DR + V
Sbjct: 67 GMLLNDRKVFV 77
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 115 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 23 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 79
Score = 28.9 bits (63), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIR 54
R ++VG E L F +G I + + GFAFV FE DAA AI
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 55 GLD 57
++
Sbjct: 63 NMN 65
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 115 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 84 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIR 54
R ++VG E L F +G I + + GFAFV FE DAA AI
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 55 GLD 57
++
Sbjct: 124 NMN 126
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 27/99 (27%), Positives = 46/99 (46%), Gaps = 12/99 (12%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIR 54
R +FVGN YE + +L+ +FS+ G + + G+ F ++D A A+R
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 55 GLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPT 93
L+ F R L V+ A E ++++ KS+ P
Sbjct: 69 NLNGREF--SGRALRVDNAASE--KNKEELKSLGTGAPV 103
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 38.1 bits (87), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 35/72 (48%), Gaps = 7/72 (9%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALEST 148
+F+ N D + + F +GN+L ++ + + FV FETQE A +A+E
Sbjct: 13 NIFIKNLDK-SIDNKALYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKM 71
Query: 149 DRSKLVDRVISV 160
+ L DR + V
Sbjct: 72 NGMLLNDRKVFV 83
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 38.1 bits (87), Expect = 0.006, Method: Composition-based stats.
Identities = 20/57 (35%), Positives = 32/57 (56%), Gaps = 8/57 (14%)
Query: 115 FEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
F P+G++ ++I R FAFV+FE E+A A+++ + S+L R I V A
Sbjct: 26 FIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 82
Score = 28.5 bits (62), Expect = 4.5, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIR 54
R ++VG E L F +G I + + GFAFV FE DAA AI
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
Query: 55 GLD 57
++
Sbjct: 66 NMN 68
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 39/85 (45%), Gaps = 9/85 (10%)
Query: 84 SKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQF 135
S + AN P L V + T ERD++ F YG + V I R FAFV F
Sbjct: 6 SGNRANPDPNCCLGVFGLS-LYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYF 64
Query: 136 ETQEEATKALESTDRSKLVDRVISV 160
E ++A +A E + +L R I V
Sbjct: 65 ENVDDAKEAKERANGMELDGRRIRV 89
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 22/47 (46%), Positives = 28/47 (59%), Gaps = 8/47 (17%)
Query: 14 TRQSELERLFSKYGRIERV----DMKS----GFAFVYFEDDRDAADA 52
T + +L +FSKYG I V D +S GFAFVYFE+ DA +A
Sbjct: 27 TTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA 73
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 35/72 (48%), Gaps = 6/72 (8%)
Query: 111 IKRHFEPYGNVLHVRI--RRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYALKDDS 168
+++ F P+G ++ +R+ + ++FV+F T E A A+ S + + + V+ +
Sbjct: 42 MRQTFSPFGQIMEIRVFPEKGYSFVRFSTHESAAHAIVSVNGTTIEGHVVKCYWG----K 97
Query: 169 ERDDRYDSPRRG 180
E D P G
Sbjct: 98 ESPDMTSGPSSG 109
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--SGFAFVYFEDDRDAADAIRGLDNIPF 61
+FVGN + + E+ +LF KYG+ V + GF F+ E A A LDN+P
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL 83
>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 = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 9/67 (13%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIR 54
R ++VGN +Y + +LE FS G I R+ + G+A++ F +R++ DA
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFA-ERNSVDAAV 95
Query: 55 GLDNIPF 61
+D F
Sbjct: 96 AMDETVF 102
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition
Motif Of Nono
Length = 99
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 2/59 (3%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--SGFAFVYFEDDRDAADAIRGLDNIPF 61
+FVGN + + E+ +LF KYG+ V + GF F+ E A A LDN+P
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMPL 76
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 66/148 (44%), Gaps = 30/148 (20%)
Query: 18 ELERLFSKYGRIERV----DMKSGF----AFVYFEDDRDAADAIRGLDNIPFGYDRRRLS 69
EL LF G I D K+G+ AFV F + D+ AI+ L+ I +RL
Sbjct: 30 ELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVLNGITV--RNKRLK 87
Query: 70 VEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN 129
V +AR G +S+ + L+V N P + + F YG+++ I R+
Sbjct: 88 VSYAR-------PGGESIKDT----NLYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRD 135
Query: 130 --------FAFVQFETQEEATKALESTD 149
AFV++ +EEA +A+ + +
Sbjct: 136 KLTGRPRGVAFVRYNKREEAQEAISALN 163
Score = 32.0 bits (71), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 19/85 (22%), Positives = 42/85 (49%), Gaps = 8/85 (9%)
Query: 87 MANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQ 138
M + R + T ++N+ P +R++ F G + RI R++ AFV F ++
Sbjct: 7 MNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSE 66
Query: 139 EEATKALESTDRSKLVDRVISVEYA 163
++ +A++ + + ++ + V YA
Sbjct: 67 XDSQRAIKVLNGITVRNKRLKVSYA 91
Score = 30.8 bits (68), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
++V N +L+ +F KYG I + ++ G AFV + +A +AI L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 57 DNIPFGYDRRRLSVEWA 73
+N+ + LSV A
Sbjct: 163 NNVIPEGGSQPLSVRLA 179
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 37.7 bits (86), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 41/148 (27%), Positives = 66/148 (44%), Gaps = 30/148 (20%)
Query: 18 ELERLFSKYGRIERV----DMKSGF----AFVYFEDDRDAADAIRGLDNIPFGYDRRRLS 69
EL LF G I D K+G+ AFV F + D+ AI+ L+ I +RL
Sbjct: 19 ELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITV--RNKRLK 76
Query: 70 VEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN 129
V +AR G +S+ + L+V N P + + F YG+++ I R+
Sbjct: 77 VSYAR-------PGGESIKDTN----LYVTNL-PRTITDDQLDTIFGKYGSIVQKNILRD 124
Query: 130 --------FAFVQFETQEEATKALESTD 149
AFV++ +EEA +A+ + +
Sbjct: 125 KLTGRPRGVAFVRYNKREEAQEAISALN 152
Score = 30.4 bits (67), Expect = 0.97, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIRGL 56
++V N +L+ +F KYG I + ++ G AFV + +A +AI L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 57 DNIPFGYDRRRLSVEWA 73
+N+ + LSV A
Sbjct: 152 NNVIPEGGSQPLSVRLA 168
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKA 144
+ T ++N+ P +R++ F G + RI R++ AFV F ++ ++ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 145 LESTDRSKLVDRVISVEYA 163
++ + + ++ + V YA
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 34/161 (21%), Positives = 69/161 (42%), Gaps = 19/161 (11%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
++VG+ YE + + + F+ +G I+ +DM GFAFV +E A A+ +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 57 DNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFE 116
+++ G ++ G+ D A R ++V + + DIK FE
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIIDQLAEEA--RAFNRIYVASVHQ-DLSDDDIKSVFE 132
Query: 117 PYGNVLHVRIRRN--------FAFVQFETQEEATKALESTD 149
+G + + R+ + F+++E + + A+ S +
Sbjct: 133 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMN 173
Score = 32.0 bits (71), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 108 ERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVIS 159
E I++ F P+G + + + + FAFV++E E A ALE + L R I
Sbjct: 27 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 86
Query: 160 V 160
V
Sbjct: 87 V 87
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRI--------ERVDMKSGFAFVYFEDDRDAADAIRGL 56
++V Q ELE+LFS+YGRI + + G F+ F+ +A +AI+GL
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 57 D 57
+
Sbjct: 151 N 151
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 144
+KT ++N+ P + + + F G + ++ R+ + FV + ++A KA
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 145 LESTDRSKLVDRVISVEYA 163
+ + + +L + I V YA
Sbjct: 61 INTLNGLRLQTKTIKVSYA 79
>pdb|1WHY|A Chain A, Solution Structure Of The Rna Recognition Motif From
Hypothetical Rna Binding Protein Bc052180
Length = 97
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 35/72 (48%), Gaps = 2/72 (2%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSG--FAFVYFEDDRDAADAIRGLDNIPFG 62
++VG T + L R F ++G I +D G FA++ +E A A + P G
Sbjct: 20 LWVGGLGPNTSLAALAREFDRFGSIRTIDHVKGDSFAYIQYESLDAAQAACAKMRGFPLG 79
Query: 63 YDRRRLSVEWAR 74
RRL V++A+
Sbjct: 80 GPDRRLRVDFAK 91
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 37/89 (41%), Gaps = 12/89 (13%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIR 54
R + V + +L +LF +YG IE V + G+ FV F+ A AI
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 55 GLDNIPFGYDRRRLSVEWARGERGRHRDG 83
GL+ F +RL V A G R G
Sbjct: 103 GLNG--FNILNKRLKVALA--ASGHQRPG 127
Score = 34.3 bits (77), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 17/75 (22%), Positives = 37/75 (49%), Gaps = 8/75 (10%)
Query: 97 FVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALEST 148
++N+ P E +++ FE YG + V+I R + FV+F++ A +A+
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 149 DRSKLVDRVISVEYA 163
+ ++++ + V A
Sbjct: 105 NGFNILNKRLKVALA 119
>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 = 37.4 bits (85), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 30/109 (27%), Positives = 49/109 (44%), Gaps = 8/109 (7%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
++R + + N Y+ E+ +F KYG I ++ + + G A+V +ED DA +A
Sbjct: 17 VNRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 76
Query: 56 LDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQ-RPTKTLFVINFDP 103
L F R L V + R + +K Q + K + IN DP
Sbjct: 77 LSG--FNVCNRYLVVLYYNANRAFQKMDTKKKEEQLKLLKEKYGINTDP 123
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/90 (23%), Positives = 48/90 (53%), Gaps = 9/90 (10%)
Query: 94 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALE 146
+ L+V N D T E +K++F+ G + +++I N+AFV++ +A AL+
Sbjct: 1 RVLYVGNLDKAIT-EDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQ 59
Query: 147 STDRSKLVDRVISVEYALKD-DSERDDRYD 175
+ + ++ + ++ + +A + S DD ++
Sbjct: 60 TLNGKQIENNIVKINWAFQSQQSSSDDTFN 89
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 37.0 bits (84), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRI--------ERVDMKSGFAFVYFEDDRDAADAIRGL 56
++V Q E+E+LFS+YGRI + + G F+ F+ +A +AI+GL
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 57 D 57
+
Sbjct: 153 N 153
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 144
+KT ++N+ P + + K F G++ ++ R+ + FV + +A KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 145 LESTDRSKLVDRVISVEYA 163
+ + + KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 37.0 bits (84), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 46/79 (58%), Gaps = 11/79 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 56 LDNIPFGYDRRRLSVEWAR 74
+ PF YD + + +++A+
Sbjct: 72 MQGFPF-YD-KPMRIQYAK 88
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/91 (26%), Positives = 43/91 (47%), Gaps = 11/91 (12%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALESTD 149
L+V N D ER +++ F P+G + ++ + F FV F + EEATKA+ +
Sbjct: 18 LYVKNLDDGIDDER-LRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 150 RSKLVDRVISVEYALKDDSERDDRYDSPRRG 180
+ + + V A + +++R P G
Sbjct: 77 GRIVATKPLYVALAQR----KEERQSGPSSG 103
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 36.6 bits (83), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/89 (29%), Positives = 42/89 (47%), Gaps = 10/89 (11%)
Query: 92 PTKTLFVINFDPIRTRERDIKRHF----EPYGNVLHVRIR----RNFAFVQFETQEEATK 143
P K L++ N P R ERD+ F E G + R+ R AF+ F +E A +
Sbjct: 24 PNKVLYLKNLSP-RVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQ 82
Query: 144 ALESTDRSKLVDRVISVEYALKDDSERDD 172
AL + KL +++ +E+ K+ +R
Sbjct: 83 ALHLVNGYKLYGKILVIEFG-KNKKQRSS 110
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 36.2 bits (82), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 66/169 (39%), Gaps = 29/169 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM----------KSGFAFVYFEDDRDAADAIR 54
+FVG + +L LF +YG + +++ G FV F + A +A
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 77
Query: 55 GLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKR 113
L N+ + ++ A E+ N + LF I + E DI+
Sbjct: 78 ALHNMKVLPGMHHPIQMKPADSEKN----------NAVEDRKLF-IGMISKKCTENDIRV 126
Query: 114 HFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVD 155
F +G + RI R AFV F T+ A A+++ +++ ++
Sbjct: 127 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTME 175
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERV-------DMKSGFAFVYFEDDRDAADAIRG 55
R +F+G + ++++ +FS +G+IE + G AFV F A AI+
Sbjct: 108 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 167
Query: 56 L 56
+
Sbjct: 168 M 168
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 35.8 bits (81), Expect = 0.025, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 32/61 (52%), Gaps = 8/61 (13%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRI--------ERVDMKSGFAFVYFEDDRDAADAIRGL 56
++V Q E+E+LFS+YGRI + + G F+ F+ +A +AI+GL
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 57 D 57
+
Sbjct: 64 N 64
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 35.8 bits (81), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 37/169 (21%), Positives = 66/169 (39%), Gaps = 29/169 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM----------KSGFAFVYFEDDRDAADAIR 54
+FVG + +L LF +YG + +++ G FV F + A +A
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQN 65
Query: 55 GLDNIPFGYDRRR-LSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKR 113
L N+ + ++ A E+ N + LF I + E DI+
Sbjct: 66 ALHNMKVLPGMHHPIQMKPADSEKN----------NAVEDRKLF-IGMISKKCTENDIRV 114
Query: 114 HFEPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSKLVD 155
F +G + RI R AFV F T+ A A+++ +++ ++
Sbjct: 115 MFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTME 163
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/61 (26%), Positives = 29/61 (47%), Gaps = 7/61 (11%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERV-------DMKSGFAFVYFEDDRDAADAIRG 55
R +F+G + ++++ +FS +G+IE + G AFV F A AI+
Sbjct: 96 RKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKA 155
Query: 56 L 56
+
Sbjct: 156 M 156
>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 = 35.4 bits (80), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 146
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 25 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 83
Query: 147 STDRSKLVDRVISVEYAL 164
+ L+ + ISV++
Sbjct: 84 GLNGQDLMGQPISVDWCF 101
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
+FV E + ++ F++YG I+ + + G+ V +E ++A A+ GL
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 57 DNIPFGYDR--RRLSVEWA 73
+ G D + +SV+W
Sbjct: 86 N----GQDLMGQPISVDWC 100
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein
U1a117, Nmr, 43 Structures
Length = 116
Score = 35.4 bits (80), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 45/79 (56%), Gaps = 11/79 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + + G AFV F++ A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 56 LDNIPFGYDRRRLSVEWAR 74
+ PF YD + + +++A+
Sbjct: 71 MQGFPF-YD-KPMRIQYAK 87
Score = 33.1 bits (74), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution
Reveals A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme
Self-Ligation Product, In Complex With U1a Rbd
Length = 97
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 71 MQGFPF-YD-KPMRIQYAKTD 89
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group
I Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 35.0 bits (79), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 46/81 (56%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + + G AFV F++ A +A+R
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 68
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 69 MQGFPF-YD-KPMRIQYAKTD 87
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 4 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 62
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 63 TNALRSMQGFPFYDKPMRIQYA-KTDSD 89
>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 = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 72 MQGFPF-YD-KPMRIQYAKTD 90
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>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 = 35.0 bits (79), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 72 MQGFPF-YD-KPMRIQYAKTD 90
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 25/80 (31%), Positives = 36/80 (45%), Gaps = 13/80 (16%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
IFVG + ++EL F K+G + V M GF F+ FED++ A+
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV--- 69
Query: 57 DNIPFGYDRRRLSVEWARGE 76
N+ F +D VE R E
Sbjct: 70 -NMHF-HDIMGKKVEVKRAE 87
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 35.0 bits (79), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 71 MQGFPF-YD-KPMRIQYAKTD 89
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>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 = 35.0 bits (79), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 7 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 66
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 67 MQGFPF-YD-KPMRIQYAKTD 85
Score = 32.3 bits (72), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 2 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 60
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 61 TNALRSMQGFPFYDKPMRIQYA-KTDSD 87
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna
Complex Reveals The Basis Of Cooperativity In
Regulation Of Polyadenylation By Human U1a Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 70
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 71 MQGFPF-YD-KPMRIQYAKTD 89
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 64
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 65 TNALRSMQGFPFYDKPMRIQYA-KTDSD 91
>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 = 35.0 bits (79), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 146
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 24 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 82
Query: 147 STDRSKLVDRVISVEYAL 164
+ L+ + ISV++
Sbjct: 83 GLNGQDLMGQPISVDWCF 100
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
+FV E + ++ F++YG I+ + + G+ V +E ++A A+ GL
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 57 DNIPFGYDR--RRLSVEWA 73
+ G D + +SV+W
Sbjct: 85 N----GQDLMGQPISVDWC 99
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 35.0 bits (79), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 71
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 72 MQGFPF-YD-KPMRIQYAKTD 90
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLYAIFSQFGQILDILVSRSLKMRGQAFVIFKEVSSA 65
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 66 TNALRSMQGFPFYDKPMRIQYA-KTDSD 92
>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 = 35.0 bits (79), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 46/81 (56%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + + G AFV F++ A +A+R
Sbjct: 6 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 65
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 66 MQGFPF-YD-KPMRIQYAKTD 84
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 1 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 59
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 60 TNALRSMQGFPFYDKPMRIQYA-KTDSD 86
>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 = 35.0 bits (79), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 47/81 (58%), Gaps = 11/81 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 8 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSATNALRS 67
Query: 56 LDNIPFGYDRRRLSVEWARGE 76
+ PF YD + + +++A+ +
Sbjct: 68 MQGFPF-YD-KPMRIQYAKTD 86
Score = 32.0 bits (71), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 3 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKMRGQAFVIFKEVSSA 61
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ + ++YA K DS+
Sbjct: 62 TNALRSMQGFPFYDKPMRIQYA-KTDSD 88
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 35.0 bits (79), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 8/57 (14%)
Query: 5 IFVGNFEYETRQSELERLFSKYGR-IERVDMKS-------GFAFVYFEDDRDAADAI 53
+FVG ++ T Q L FS+YG ++ V MK GF FV F+D +
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVL 75
>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 = 34.7 bits (78), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 10/77 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIE--RV--DMKS----GFAFVYFEDDRDAADAIRGL 56
+FVG+ E +++ F+ +GRI RV DM + G+ FV F + DA +AI+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 57 DNIPFGYDRRRLSVEWA 73
G R++ WA
Sbjct: 78 GGQWLG--GRQIRTNWA 92
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 38/89 (42%), Gaps = 9/89 (10%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNFA--------FVQFETQEEATKALES 147
+FV + P T E DIK F P+G + R+ ++ A FV F + +A A++
Sbjct: 18 VFVGDLSPEITTE-DIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 148 TDRSKLVDRVISVEYALKDDSERDDRYDS 176
L R I +A + Y+S
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPKSTYES 105
>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 = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 146
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 11 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 69
Query: 147 STDRSKLVDRVISVEYAL 164
+ L+ + ISV++
Sbjct: 70 GLNGQDLMGQPISVDWCF 87
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
+FV E + ++ F++YG I+ + + G+ V +E ++A A+ GL
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 57 DNIPFGYDR--RRLSVEWA 73
+ G D + +SV+W
Sbjct: 72 N----GQDLMGQPISVDWC 86
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 34.7 bits (78), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 39/83 (46%), Gaps = 8/83 (9%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKALEST 148
LFV +T E D+++ FEP+G + + R AFV+F+T EA A+ +
Sbjct: 15 LFVGMLGKQQTDE-DVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 149 DRSKLVDRVISVEYALKDDSERD 171
S+ + S D+E++
Sbjct: 74 HSSRTLPGASSSLVVKFADTEKE 96
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 34.3 bits (77), Expect = 0.066, Method: Compositional matrix adjust.
Identities = 29/93 (31%), Positives = 42/93 (45%), Gaps = 11/93 (11%)
Query: 77 RGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNF 130
RG H + N+ K L V N P R R+ D+++ F +G +L V I + F
Sbjct: 17 RGSHMN----TENKSQPKRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGF 71
Query: 131 AFVQFETQEEATKALESTDRSKLVDRVISVEYA 163
FV FE +A +A E + + R I V A
Sbjct: 72 GFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM------KSGFAFVYFEDDRDA 49
+ V N + R +L ++F ++G+I V++ GF FV FE+ DA
Sbjct: 32 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 82
>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 = 34.3 bits (77), Expect = 0.067, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 146
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 147 STDRSKLVDRVISVEYAL 164
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
Score = 29.3 bits (64), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
+FV E + ++ F++YG I+ + + G+ V +E ++A A+ GL
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 57 DNIPFGYDR--RRLSVEWA 73
+ G D + +SV+W
Sbjct: 70 N----GQDLMGQPISVDWC 84
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 34.3 bits (77), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 2/57 (3%)
Query: 3 RPIFVGNFEYETRQSELERLFS--KYGRIERVDMKSGFAFVYFEDDRDAADAIRGLD 57
+ ++V N T + +E+ F+ K G +ERV +AFV+F + DA +A++ L+
Sbjct: 16 KILYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALN 72
Score = 31.6 bits (70), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 37/73 (50%), Gaps = 3/73 (4%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPY--GNVLHVRIRRNFAFVQFETQEEATKALESTDR 150
K L+V N + T E I++ F G V V+ R++AFV F +E+A +A+++ +
Sbjct: 15 VKILYVRNL-MLSTSEEMIEKEFNNIKPGAVERVKKIRDYAFVHFSNREDAVEAMKALNG 73
Query: 151 SKLVDRVISVEYA 163
L I V A
Sbjct: 74 KVLDGSPIEVTLA 86
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 34.3 bits (77), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFED 45
+R I+VGN +Y ELE F G + RV + GFA++ F D
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 57
>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 = 34.3 bits (77), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
SR +++G+ Y+ + ++ L S G + + M G+AF+ F D +A A+
Sbjct: 3 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 62
Query: 54 RGLDNIPFG 62
R L+ G
Sbjct: 63 RNLNGYQLG 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 = 34.3 bits (77), Expect = 0.081, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 38/66 (57%), Gaps = 9/66 (13%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRI-ERVDMKS----GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL+R LFS++G + + V +K+ G AFV F++ + +A+R
Sbjct: 9 IYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMKMRGQAFVIFKELGSSTNALRQ 68
Query: 56 LDNIPF 61
L PF
Sbjct: 69 LQGFPF 74
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.9 bits (76), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
SR +++G+ Y+ + ++ L S G + + M G+AF+ F D +A A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 54 RGLDNIPFG 62
R L+ G
Sbjct: 62 RNLNGYQLG 70
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 33.9 bits (76), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 46/103 (44%), Gaps = 23/103 (22%)
Query: 94 KTLFV--INFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATK 143
KT+F+ ++FD + E + + +G++ +VR+ + AF QF TQE A K
Sbjct: 16 KTVFIRNLSFD---SEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAAQK 72
Query: 144 ALESTDRS------KLVDRVISVEYALKDDSERDDRYDSPRRG 180
L + KL R + V+ A+ RD+ P G
Sbjct: 73 CLAAASLEAEGGGLKLDGRQLKVDLAVT----RDEAASGPSSG 111
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.9 bits (76), Expect = 0.091, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
+FV N Y + + +LE+LFS YG + + GFAFV F A A +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEV 70
Query: 57 DNIPF 61
D F
Sbjct: 71 DGQVF 75
>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 = 33.9 bits (76), Expect = 0.094, Method: Compositional matrix adjust.
Identities = 33/161 (20%), Positives = 67/161 (41%), Gaps = 19/161 (11%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
++VG+ YE + + + F+ +G I+ +D GFAFV +E A A+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 57 DNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHFE 116
+++ G ++ G+ D A R ++V + + DIK FE
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIIDQLAEEA--RAFNRIYVASVHQ-DLSDDDIKSVFE 131
Query: 117 PYGNVLHVRIRRN--------FAFVQFETQEEATKALESTD 149
+G + + R+ + F+++E + + A+ S +
Sbjct: 132 AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXN 172
Score = 30.8 bits (68), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 108 ERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALESTDRSKLVDRVIS 159
E I++ F P+G + + + FAFV++E E A ALE + L R I
Sbjct: 26 EDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIK 85
Query: 160 V 160
V
Sbjct: 86 V 86
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 33.9 bits (76), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 8/52 (15%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFED 45
+R I+VGN +Y ELE F G + RV + GFA++ F D
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSD 56
>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 = 33.9 bits (76), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 37/78 (47%), Gaps = 9/78 (11%)
Query: 95 TLFVINFDPIRTRERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALE 146
LFV T E DI F YG + +H+ + R + V++ET +EA A+E
Sbjct: 9 ILFVTGVHEEATEE-DIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME 67
Query: 147 STDRSKLVDRVISVEYAL 164
+ L+ + ISV++
Sbjct: 68 GLNGQDLMGQPISVDWCF 85
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 14/79 (17%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
+FV E + ++ F++YG I+ + + G+ V +E ++A A+ GL
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 57 DNIPFGYDR--RRLSVEWA 73
+ G D + +SV+W
Sbjct: 70 N----GQDLMGQPISVDWC 84
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-----GFAFVYFEDDRDAADAIRG 55
++R +++ N Y+ E+ +F KYG I ++ + + G A+V +ED DA +A
Sbjct: 11 VNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDH 70
Query: 56 LDNIPFGYDRRRLSVEW 72
L F R L V +
Sbjct: 71 LSG--FNVCNRYLVVLY 85
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 33.5 bits (75), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 29/64 (45%), Gaps = 7/64 (10%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDMK-------SGFAFVYFEDDRDAADAIRG 55
R +FVGN E R+ L LF + G + +V + F FV F+ + AI
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIAL 76
Query: 56 LDNI 59
L+ I
Sbjct: 77 LNGI 80
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 34/79 (43%), Gaps = 7/79 (8%)
Query: 83 GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRR-------NFAFVQF 135
GS Q P+ + + E D++R FE +GN+ I R AFV++
Sbjct: 4 GSSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKY 63
Query: 136 ETQEEATKALESTDRSKLV 154
+ EA A+ + S+ +
Sbjct: 64 SSHAEAQAAINALHGSQTM 82
Score = 33.5 bits (75), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM-------KSGFAFVYFEDDRDAADAIRG 55
R +FVG + + ++ RLF +G IE + G AFV + +A AI
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 56 L 56
L
Sbjct: 76 L 76
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 10/70 (14%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 11 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRS 70
Query: 56 LDNIPFGYDR 65
PF YD+
Sbjct: 71 XQGFPF-YDK 79
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 6 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 64
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ ++YA K DS+
Sbjct: 65 TNALRSXQGFPFYDKPXRIQYA-KTDSD 91
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 10/70 (14%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 12 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRS 71
Query: 56 LDNIPFGYDR 65
PF YD+
Sbjct: 72 XQGFPF-YDK 80
Score = 30.4 bits (67), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 7 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 65
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ ++YA K DS+
Sbjct: 66 TNALRSXQGFPFYDKPXRIQYA-KTDSD 92
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.5 bits (75), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 39/70 (55%), Gaps = 10/70 (14%)
Query: 5 IFVGNFEYETRQSELER----LFSKYGRIERV----DMKS-GFAFVYFEDDRDAADAIRG 55
I++ N + ++ EL++ +FS++G+I + +K G AFV F++ A +A+R
Sbjct: 9 IYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSATNALRS 68
Query: 56 LDNIPFGYDR 65
PF YD+
Sbjct: 69 XQGFPF-YDK 77
Score = 30.8 bits (68), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 44/88 (50%), Gaps = 11/88 (12%)
Query: 91 RPTKTLFVINFDPIRTRERDIKRH----FEPYGNVLHVRIRRNF-----AFVQFETQEEA 141
RP T+++ N + + ++ ++K+ F +G +L + + R+ AFV F+ A
Sbjct: 4 RPNHTIYINNLNE-KIKKDELKKSLHAIFSRFGQILDILVSRSLKXRGQAFVIFKEVSSA 62
Query: 142 TKALESTDRSKLVDRVISVEYALKDDSE 169
T AL S D+ ++YA K DS+
Sbjct: 63 TNALRSXQGFPFYDKPXRIQYA-KTDSD 89
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 36/76 (47%), Gaps = 7/76 (9%)
Query: 94 KTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI------RRNFAFVQFETQEEATKALES 147
K L V N P R R+ D+++ F +G +L V I + F FV FE +A +A E
Sbjct: 16 KRLHVSNI-PFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREK 74
Query: 148 TDRSKLVDRVISVEYA 163
+ + R I V A
Sbjct: 75 LHGTVVEGRKIEVNNA 90
Score = 31.6 bits (70), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 27/51 (52%), Gaps = 6/51 (11%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM------KSGFAFVYFEDDRDA 49
+ V N + R +L ++F ++G+I V++ GF FV FE+ DA
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADA 68
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 38/77 (49%), Gaps = 10/77 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIE--RV--DMKS----GFAFVYFEDDRDAADAIRGL 56
+FVG+ E +++ F+ +G+I RV DM + G+ FV F + DA +AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 57 DNIPFGYDRRRLSVEWA 73
G R++ WA
Sbjct: 78 GGQWLG--GRQIRTNWA 92
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 47/172 (27%), Positives = 69/172 (40%), Gaps = 33/172 (19%)
Query: 5 IFVGNFEYE--TRQSELERLFSKYGRIERVDM---KSGFAFVYFEDDRDAADAIRGLD-- 57
+ V N E T QS L LF YG ++RV + K A V D A A+ L+
Sbjct: 37 LLVSNLNPERVTPQS-LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 95
Query: 58 ---------------NIPF---GYDRRRLSVEWARGERGRHRD-GSKSMANQ-RPTKTLF 97
N+ G + + L+ ++ R + GSK+ N P+ TL
Sbjct: 96 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 155
Query: 98 VINFDPIRTRERDIKRHFEPYGNVLH----VRIRRNFAFVQFETQEEATKAL 145
+ N P E D+K F G V+ + R A +Q + EEA +AL
Sbjct: 156 LSNIPP-SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 206
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 33.1 bits (74), Expect = 0.17, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM---------KSGFAFVYFEDDRDAADAIRG 55
+ +G + + +FS YG+I+ +DM G+A+V FE+ +A A++
Sbjct: 7 VHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKH 66
Query: 56 LD 57
+D
Sbjct: 67 MD 68
Score = 29.3 bits (64), Expect = 2.6, Method: Composition-based stats.
Identities = 13/43 (30%), Positives = 25/43 (58%)
Query: 122 LHVRIRRNFAFVQFETQEEATKALESTDRSKLVDRVISVEYAL 164
+H + + +A+V+FE +EA KAL+ D ++ + I+ L
Sbjct: 41 MHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQEITATAVL 83
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 30/68 (44%), Gaps = 11/68 (16%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIER-----------VDMKSGFAFVYFEDDRDAA 50
S +F+ N + T + L+ +FSK G I+ V + GF FV ++ A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 51 DAIRGLDN 58
A++ L
Sbjct: 65 KALKQLQG 72
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 32.7 bits (73), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 47/172 (27%), Positives = 69/172 (40%), Gaps = 33/172 (19%)
Query: 5 IFVGNFEYE--TRQSELERLFSKYGRIERVDM---KSGFAFVYFEDDRDAADAIRGLD-- 57
+ V N E T QS L LF YG ++RV + K A V D A A+ L+
Sbjct: 6 LLVSNLNPERVTPQS-LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGH 64
Query: 58 ---------------NIPF---GYDRRRLSVEWARGERGRHRD-GSKSMANQ-RPTKTLF 97
N+ G + + L+ ++ R + GSK+ N P+ TL
Sbjct: 65 KLHGKPIRITLSKHQNVQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLH 124
Query: 98 VINFDPIRTRERDIKRHFEPYGNVLH----VRIRRNFAFVQFETQEEATKAL 145
+ N P E D+K F G V+ + R A +Q + EEA +AL
Sbjct: 125 LSNIPP-SVSEEDLKVLFSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQAL 175
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-------GFAFVYFEDDRDAADAI 53
M +FVG + ++E+ F++YG ++ V + + G+ FV F +D D +
Sbjct: 8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Query: 54 RGLDN 58
N
Sbjct: 68 ESQIN 72
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 34/70 (48%), Gaps = 3/70 (4%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--FAFVQFETQEEATKALESTDRSKL 153
LFV N P E D KR FE YG V I R+ F F++ E++ A A D + L
Sbjct: 25 LFVGNL-PTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTIL 83
Query: 154 VDRVISVEYA 163
R + + +A
Sbjct: 84 KSRPLRIRFA 93
Score = 28.9 bits (63), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--SGFAFVYFEDDRDAADAIRGLD 57
+FVGN + + + +RLF +YG V + GF F+ E A A LD
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELD 79
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 36/164 (21%), Positives = 63/164 (38%), Gaps = 27/164 (16%)
Query: 6 FVGNFEYETRQSELERLFSKYGRIERVDM----------KSGFAFVYFEDDRDAADAIRG 55
FVG + +L LF +YG + +++ G FV F + A +A
Sbjct: 7 FVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQNA 66
Query: 56 LDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKRHF 115
L N ++ + + D K+ N + LF+ + E DI+ F
Sbjct: 67 LHN-------XKVLPGXHHPIQXKPADSEKN--NAVEDRKLFIGXISK-KCTENDIRVXF 116
Query: 116 EPYGNVLHVRI-------RRNFAFVQFETQEEATKALESTDRSK 152
+G + RI R AFV F T+ A A+++ +++
Sbjct: 117 SSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKAXHQAQ 160
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 15/60 (25%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-------GFAFVYFEDDRDAADAI 53
M +FVG + ++E+ F++YG ++ V + + G+ FV F +D D +
Sbjct: 9 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 68
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 8/61 (13%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
++VG+ + + L +F +GRIE + + G+ F+ F D A A+ L
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 57 D 57
+
Sbjct: 89 N 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 32.3 bits (72), Expect = 0.30, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN--------FAFVQFETQEEATKA 144
+KT ++N+ P + + K F G++ ++ R+ + FV + +A KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 145 LESTDRSKLVDRVISVEYA 163
+ + + KL + I V YA
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 40/84 (47%), Gaps = 12/84 (14%)
Query: 88 ANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQE 139
A +P+KTLFV T E +K F+ + RI + F FV F ++E
Sbjct: 10 ARSQPSKTLFVKGLSE-DTTEETLKESFD---GSVRARIVTDRETGSSKGFGFVDFNSEE 65
Query: 140 EATKALESTDRSKLVDRVISVEYA 163
+A A E+ + ++ +++++A
Sbjct: 66 DAKAAKEAMEDGEIDGNKVTLDWA 89
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 34/78 (43%), Gaps = 7/78 (8%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVD-----MKSGFAFVYFEDDRDAADAIRGL 56
S+ +FV +T + L+ F R V GF FV F + DA A +
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 57 DNIPFGYDRRRLSVEWAR 74
++ D +++++WA+
Sbjct: 75 EDGEI--DGNKVTLDWAK 90
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 29/60 (48%), Gaps = 7/60 (11%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDM------KS-GFAFVYFEDDRDAADAI 53
+ +FV N +Y+ +L+ +FS G + R D+ KS G V FE +A AI
Sbjct: 14 LGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAI 73
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 32.0 bits (71), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 16/65 (24%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 1 MSRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS-------GFAFVYFEDDRDAADAI 53
M +FVG + ++E+ F++YG ++ V + + G+ FV F +D D +
Sbjct: 8 MPNTVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIV 67
Query: 54 RGLDN 58
N
Sbjct: 68 ESQIN 72
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 32.0 bits (71), Expect = 0.37, Method: Composition-based stats.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 8/63 (12%)
Query: 108 ERDIKRHFEPYGNV--LHVRIRR------NFAFVQFETQEEATKALESTDRSKLVDRVIS 159
E DI F YG + +H+ + R + V++ET +EA A+E + L+ + IS
Sbjct: 21 EEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQPIS 80
Query: 160 VEY 162
V++
Sbjct: 81 VDW 83
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 33/170 (19%), Positives = 66/170 (38%), Gaps = 36/170 (21%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAI 53
S +F+G ++T + L F KYG + + + GF F+ FE + +
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 54 RGLDNIPFGYDRRRLSVEWARGERGRHRDGSKSMANQRPTKTLFVINFDPIRTRERDIKR 113
+ + L + +R RD Q T +FV P R ++ +
Sbjct: 63 K---------TQHILDGKVIDPKRAIPRD------EQDKTGKIFVGGIGP-DVRPKEFEE 106
Query: 114 HFEPYGNVLHVRIR--------RNFAFVQFETQEEATKALESTDRSKLVD 155
F +G ++ ++ R F FV +++ + A++ ++K +D
Sbjct: 107 FFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSAD----AVDRVCQNKFID 152
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 32.0 bits (71), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRIERVDM-------KSGFAFVYFEDDRDAADAIRG 55
R +FVG + + ++ RLF +G I+ + G AFV F +A AI
Sbjct: 16 RKLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHA 75
Query: 56 L 56
L
Sbjct: 76 L 76
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 32.0 bits (71), Expect = 0.40, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKS---GFAFVYFEDDRDA 49
+FVG + EL++ F +YG + V + FAFV F DD+ A
Sbjct: 14 VFVGRCTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVA 61
>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 = 32.0 bits (71), Expect = 0.42, Method: Composition-based stats.
Identities = 18/69 (26%), Positives = 33/69 (47%), Gaps = 8/69 (11%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
SR +++G+ Y+ + ++ L S G + + M G+AF+ F D +A A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 54 RGLDNIPFG 62
R L+ G
Sbjct: 64 RNLNGYQLG 72
>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 = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 35/77 (45%), Gaps = 8/77 (10%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
++V N +L+ +F KYG I + ++ G AFV + +A +AI L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 57 DNIPFGYDRRRLSVEWA 73
+N+ + LSV A
Sbjct: 76 NNVIPEGGSQPLSVRLA 92
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 31.6 bits (70), Expect = 0.53, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDMKS---GFAFVYFEDDRDA 49
S +FVG + + EL FS+YG + V + FAFV F DD+ A
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIA 55
>pdb|2K3K|A Chain A, Solution Structure Of Drosophila Melanogaster Snf Rbd1
Length = 104
Score = 31.6 bits (70), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 33/53 (62%), Gaps = 6/53 (11%)
Query: 18 ELERLFSKYGRI-ERVDMKS----GFAFVYFEDDRDAADAIRGLDNIPFGYDR 65
L +FS++G+I + V +K+ G AFV F++ A++A+R + PF YD+
Sbjct: 26 SLYAIFSQFGQILDIVALKTLKMRGQAFVIFKEIGSASNALRTMQGFPF-YDK 77
>pdb|4GED|A Chain A, Crystal Structure Of The Leishmania Major
Peroxidase-Cytochrome C Complex
Length = 268
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNIPFGYD 64
++ GN + + LE L KY +I D+ A+V E G IPF +
Sbjct: 61 LYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIE--------YMGGPTIPFCWG 112
Query: 65 RRRLSVEWARGERGRHRDGSKSMANQR 91
R G GR DGSK+ ++ R
Sbjct: 113 RVDAKDGSVCGPDGRLPDGSKTQSHVR 139
>pdb|3RIW|A Chain A, The Crystal Structure Of Leishmania Major Peroxidase
Mutant C197t
pdb|3RIW|B Chain B, The Crystal Structure Of Leishmania Major Peroxidase
Mutant C197t
Length = 271
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNIPFGYD 64
++ GN + + LE L KY +I D+ A+V E G IPF +
Sbjct: 62 LYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIE--------YMGGPTIPFCWG 113
Query: 65 RRRLSVEWARGERGRHRDGSKSMANQR 91
R G GR DGSK+ ++ R
Sbjct: 114 RVDAKDGSVCGPDGRLPDGSKTQSHVR 140
>pdb|3RIV|A Chain A, The Crystal Structure Of Leishmania Major Peroxidase
pdb|3RIV|B Chain B, The Crystal Structure Of Leishmania Major Peroxidase
Length = 271
Score = 30.4 bits (67), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 36/87 (41%), Gaps = 8/87 (9%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNIPFGYD 64
++ GN + + LE L KY +I D+ A+V E G IPF +
Sbjct: 62 LYAGNKGLDIPRKALETLKKKYPQISYADLWVLAAYVAIE--------YMGGPTIPFCWG 113
Query: 65 RRRLSVEWARGERGRHRDGSKSMANQR 91
R G GR DGSK+ ++ R
Sbjct: 114 RVDAKDGSVCGPDGRLPDGSKTQSHVR 140
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 10/78 (12%)
Query: 96 LFVINFDPIRTRERDIKRHFEPYG-NVLHVRIRRN--------FAFVQFETQEEATKALE 146
+ ++ P E DI+ + +G VR+ RN FAFV+F ++AT+ +E
Sbjct: 3 IVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
Query: 147 STDRS-KLVDRVISVEYA 163
+ S ++ + +S+ Y+
Sbjct: 63 ANQHSLNILGQKVSMHYS 80
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 5 IFVGNFEYETRQSELERLFS--KYGRIERVDMKSGFAFVYFEDDRDAADAIRGL 56
+++GN +L +LF K +V +KSG+AFV + D A AI L
Sbjct: 11 LYIGNLSPAVTADDLRQLFGDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIETL 64
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAIRGL 56
+FV + E ++ E++ F YG I+ + + G+A V +E + A A L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 57 DNIPFGYDRRRLSVEWA 73
+ + + V+W
Sbjct: 89 NGAEIM--GQTIQVDWC 103
>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 = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/77 (22%), Positives = 33/77 (42%), Gaps = 10/77 (12%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFEDDRDAADAIRGL 56
+FV + E ++ E++ F YG I+ + + G+A V +E + A A L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 57 DNIPFGYDRRRLSVEWA 73
+ + + V+W
Sbjct: 135 NGAEIM--GQTIQVDWC 149
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 34/72 (47%), Gaps = 8/72 (11%)
Query: 83 GSKSMANQRPTKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF-------AFVQF 135
G + N +++++ F P DIK E G VL++++RR FV F
Sbjct: 1 GRWILKNDVKNRSVYIKGF-PTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVF 59
Query: 136 ETQEEATKALES 147
++ E A K +E+
Sbjct: 60 DSIESAKKFVET 71
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 10/62 (16%)
Query: 3 RPIFVGNFEYETRQSELERLFSKYGRI-ERVDMKS-------GFAFVYFED--DRDAADA 52
R +F+G +ET + L + ++G++ + V M+ GF FV F + DAA A
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 53 IR 54
R
Sbjct: 88 AR 89
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 11/77 (14%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIRGL 56
IFVG Y T + L + F +G IE + + G+ FV D A A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKDP 79
Query: 57 DNIPFGYDRRRLSVEWA 73
+ I D R+ +V A
Sbjct: 80 NPI---IDGRKANVNLA 93
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 29.3 bits (64), Expect = 2.7, Method: Composition-based stats.
Identities = 14/49 (28%), Positives = 26/49 (53%), Gaps = 8/49 (16%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRIERVDMK--------SGFAFVYFED 45
+F+G ++T + +L+ FSK+G + +K GF FV F++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKE 50
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.9 bits (63), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/79 (21%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRNF--------AFVQFETQEEATKA 144
+ T ++N+ P +R++ F G + RI R++ AFV F ++ ++ +A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 145 LESTDRSKLVDRVISVEYA 163
++ + + ++ + V YA
Sbjct: 62 IKVLNGITVRNKRLKVSYA 80
>pdb|1VHH|A Chain A, A Potential Catalytic Site Within The Amino-Terminal
Signalling Domain Of Sonic Hedgehog
Length = 162
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 24 SKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNI 59
SKYG + R+ +++GF +VY+E +++ +++
Sbjct: 124 SKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSV 159
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 110 DIKRHFEPYGNVLHVRIRRNF-------AFVQFETQEEATKALES 147
DIK E G VL++++RR FV F++ E A K +E+
Sbjct: 125 DIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVET 169
>pdb|3HO5|H Chain H, Crystal Structure Of Hedgehog-interacting Protein (hhip)
And Sonic Hedgehog (shh) Complex
pdb|3MXW|A Chain A, Crystal Structure Sonic Hedgehog Bound To The 5e1 Fab
Fragment
Length = 169
Score = 28.5 bits (62), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 24 SKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNI 59
SKYG + R+ +++GF +VY+E +++ +++
Sbjct: 128 SKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSV 163
>pdb|3N1R|A Chain A, Crystal Structure Of Shhn
Length = 160
Score = 28.5 bits (62), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 24 SKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNI 59
SKYG + R+ +++GF +VY+E +++ +++
Sbjct: 122 SKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSV 157
>pdb|3M1N|A Chain A, Crystal Structure Of Human Sonic Hedgehog N-Terminal
Domain
pdb|3M1N|B Chain B, Crystal Structure Of Human Sonic Hedgehog N-Terminal
Domain
Length = 175
Score = 28.5 bits (62), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 24 SKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNI 59
SKYG + R+ +++GF +VY+E +++ +++
Sbjct: 134 SKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSV 169
>pdb|2WG4|A Chain A, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Sonic Hedgehog Without
Calcium
Length = 155
Score = 28.5 bits (62), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/36 (27%), Positives = 23/36 (63%)
Query: 24 SKYGRIERVDMKSGFAFVYFEDDRDAADAIRGLDNI 59
SKYG + R+ +++GF +VY+E +++ +++
Sbjct: 118 SKYGMLARLAVEAGFDWVYYESKAHIHCSVKAENSV 153
>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 = 28.5 bits (62), Expect = 4.3, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 32/69 (46%), Gaps = 11/69 (15%)
Query: 6 FVGNFEYETRQSELERLFSKYGRIERVDMKS--------GFAFVYFEDDRDAADAIRGLD 57
FVG ++T + +L+ F+K+G + +K GF F+ F +DAA + LD
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILF---KDAASVEKVLD 71
Query: 58 NIPFGYDRR 66
D R
Sbjct: 72 QKEHRLDGR 80
>pdb|2WFX|A Chain A, Crystal Structure Of The Complex Between Human Hedgehog-
Interacting Protein Hip And Sonic Hedgehog In The
Presence Of Calcium
Length = 152
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 10/21 (47%), Positives = 17/21 (80%)
Query: 24 SKYGRIERVDMKSGFAFVYFE 44
SKYG + R+ +++GF +VY+E
Sbjct: 118 SKYGMLARLAVEAGFDWVYYE 138
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 14/65 (21%), Positives = 29/65 (44%), Gaps = 8/65 (12%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRIERVDM--------KSGFAFVYFEDDRDAADAI 53
S ++VG+ + + L +F +G+I+ + + G+ F+ F D A A+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 54 RGLDN 58
L+
Sbjct: 65 EQLNG 69
>pdb|3D1M|A Chain A, Crystal Structure Of Sonic Hedgehog Bound To The Third
Fniii Domain Of Cdo
pdb|3D1M|B Chain B, Crystal Structure Of Sonic Hedgehog Bound To The Third
Fniii Domain Of Cdo
Length = 168
Score = 28.1 bits (61), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 25/39 (64%), Gaps = 3/39 (7%)
Query: 9 NFEYETRQSEL---ERLFSKYGRIERVDMKSGFAFVYFE 44
+ YE R ++ +R SKYG + R+ +++GF +VY+E
Sbjct: 118 SLHYEGRAVDITTSDRDRSKYGMLARLAVEAGFDWVYYE 156
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 39/77 (50%), Gaps = 11/77 (14%)
Query: 93 TKTLFVINFDPIRTRERDIKRHFEPYGNVLHVRIRRN-------FAFVQFETQEEATKAL 145
+KTL + N T E ++ FE +++ +N +AF++F + E+A +AL
Sbjct: 15 SKTLVLSNLSYSATEE-TLQEVFE---KATFIKVPQNQNGKSKGYAFIEFASFEDAKEAL 70
Query: 146 ESTDRSKLVDRVISVEY 162
S ++ ++ R I +E
Sbjct: 71 NSCNKREIEGRAIRLEL 87
Score = 27.7 bits (60), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 20/78 (25%), Positives = 35/78 (44%), Gaps = 4/78 (5%)
Query: 2 SRPIFVGNFEYETRQSELERLFSKYGRI---ERVDMKS-GFAFVYFEDDRDAADAIRGLD 57
S+ + + N Y + L+ +F K I + + KS G+AF+ F DA +A+ +
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 58 NIPFGYDRRRLSVEWARG 75
RL ++ RG
Sbjct: 75 KREIEGRAIRLELQGPRG 92
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 27.7 bits (60), Expect = 6.4, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 104 IRTRERDIKRHFEPYGNVLHVRI--------RRNFAFVQFETQEEATKALE 146
+ T D+K +FE +G V + R F FV FE+++ K E
Sbjct: 9 VNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCE 59
>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 = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRI--------ERVDMKSGFAFVYFEDDRDAADAIRGL 56
+++ Q ++E +FS++GRI + + G AF+ F+ +A +AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 57 D 57
+
Sbjct: 151 N 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 14/61 (22%), Positives = 29/61 (47%), Gaps = 8/61 (13%)
Query: 5 IFVGNFEYETRQSELERLFSKYGRI--------ERVDMKSGFAFVYFEDDRDAADAIRGL 56
+++ Q ++E +FS++GRI + + G AF+ F+ +A +AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 57 D 57
+
Sbjct: 151 N 151
>pdb|2QHP|A Chain A, Crystal Structure Of Fructokinase (Np_810670.1) From
Bacteroides Thetaiotaomicron Vpi-5482 At 1.80 A
Resolution
Length = 296
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 3/67 (4%)
Query: 7 VGNFEYETRQSELERLFSKYGRIERVDMKSGFAFVYFEDDRDAADAIR---GLDNIPFGY 63
VGN E E+ + +IERVD +G V +D+ I+ DNIPF
Sbjct: 47 VGNDELGDEIXEVFKEKQLKNQIERVDYPTGTVQVTLDDEGVPCYEIKEGVAWDNIPFTD 106
Query: 64 DRRRLSV 70
+ +RL++
Sbjct: 107 ELKRLAL 113
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.140 0.421
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,641,084
Number of Sequences: 62578
Number of extensions: 300787
Number of successful extensions: 865
Number of sequences better than 100.0: 168
Number of HSP's better than 100.0 without gapping: 70
Number of HSP's successfully gapped in prelim test: 98
Number of HSP's that attempted gapping in prelim test: 662
Number of HSP's gapped (non-prelim): 270
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)