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= 038096
(211 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 74.3 bits (181), Expect = 5e-14, Method: Compositional matrix adjust.
Identities = 33/77 (42%), Positives = 54/77 (70%), Gaps = 1/77 (1%)
Query: 28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
N VY+G LDEKV+E +L+++ +QAG VV+ ++P+D+ T + +G+ FVE+ SEE Y
Sbjct: 13 NQDATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADY 72
Query: 88 AIKLFSGIVTLYNRTLR 104
AIK+ ++ LY + +R
Sbjct: 73 AIKIMD-MIKLYGKPIR 88
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 59.3 bits (142), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 33/85 (38%), Positives = 51/85 (60%), Gaps = 1/85 (1%)
Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
SG + + +Y+G L E+V+++VL+ I G + D+ IP D ET+K +GFAFVE+E E
Sbjct: 6 SGMATTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAE 65
Query: 84 IGHYAIKLFSGIVTLYNRTLRFALS 108
AI + L+ RT+R L+
Sbjct: 66 DAAAAIDNMNE-SELFGRTIRVNLA 89
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 58.9 bits (141), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 30/72 (41%), Positives = 46/72 (63%), Gaps = 2/72 (2%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
V++GNL+ +V E +LY++ +QAG + + I +D+E KPK F FV ++ E YAI L
Sbjct: 18 TVFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIAL 76
Query: 92 FSGIVTLYNRTL 103
+GI LY R +
Sbjct: 77 LNGI-RLYGRPI 87
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 58.2 bits (139), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+Y+G L E+V+++VL+ I G + D+ IP D ET+K +GFAFVE+E E AI
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 93 SGIVTLYNRTLRFALS 108
+ L+ RT+R L+
Sbjct: 126 NE-SELFGRTIRVNLA 140
>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 = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+Y+G L E+V+++VL+ I G + D+ IP D ET+K +GFAFVE+E E AI
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 93 SGIVTLYNRTLRFALS 108
+ L+ RT+R L+
Sbjct: 70 NE-SELFGRTIRVNLA 84
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+Y+G L E+V+++VL+ I G + D+ IP D ET+K +GFAFVE+E E AI
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 93 SGIVTLYNRTLRFALS 108
+ L+ RT+R L+
Sbjct: 68 NE-SELFGRTIRVNLA 82
>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 = 56.2 bits (134), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+Y+G L E+V+++VL+ I G + D+ IP D ET+K +GFAFVE+E E AI
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 93 SGIVTLYNRTLRFALS 108
+ L+ RT+R L+
Sbjct: 65 NE-SELFGRTIRVNLA 79
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/84 (33%), Positives = 45/84 (53%), Gaps = 1/84 (1%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
+V++GN+ + E L DI + G VV + D+ET KPKG+ F EY+ +E A++
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRN 69
Query: 92 FSGIVTLYNRTLRFALSGQDKNAQ 115
+G R LR + +KN +
Sbjct: 70 LNG-REFSGRALRVDNAASEKNKE 92
>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 = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 10 VPNDVVSRNKRQIMS-----GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR 64
V N + RNKR +S G S N+Y+ NL + + L I + G +V I R
Sbjct: 75 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 134
Query: 65 DKETDKPKGFAFVEYESEEIGHYAIKLFSGIV 96
DK T +P+G AFV Y E AI + ++
Sbjct: 135 DKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/85 (30%), Positives = 44/85 (51%), Gaps = 1/85 (1%)
Query: 22 IMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
+M+ S N+ + L + +R LY + G + I RD +T G+AFV++ S
Sbjct: 6 LMNDPRASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTS 65
Query: 82 EEIGHYAIKLFSGIVTLYNRTLRFA 106
E AIK+ +GI T+ N+ L+ +
Sbjct: 66 EXDSQRAIKVLNGI-TVRNKRLKVS 89
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 48.1 bits (113), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 5/92 (5%)
Query: 10 VPNDVVSRNKRQIMS-----GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPR 64
V N + RNKR +S G S N+Y+ NL + + L I + G +V I R
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILR 123
Query: 65 DKETDKPKGFAFVEYESEEIGHYAIKLFSGIV 96
DK T +P+G AFV Y E AI + ++
Sbjct: 124 DKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
S N+ + L + + +R LY + G + I RD +T G+AFV++ SE A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 89 IKLFSGIVTLYNRTLRFA 106
IK+ +GI T+ N+ L+ +
Sbjct: 62 IKVLNGI-TVRNKRLKVS 78
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 47.8 bits (112), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N+Y+GNL + ++ Q G+V ++ + D+ET KPKGF FVE + E + KL
Sbjct: 3 NIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAKL 62
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 47.4 bits (111), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 31/96 (32%), Positives = 51/96 (53%), Gaps = 4/96 (4%)
Query: 26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDL-YIPRDKETDKPKGFAFVEYESEEI 84
S+ ++IGNLD +++E++LYD G ++ I RD +T KG+AF+ + S +
Sbjct: 1 GSSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDA 60
Query: 85 GHYAIKLFSGIVTLYNR--TLRFALSGQDKNAQNSS 118
AI+ +G L NR T+ +A K + SS
Sbjct: 61 SDAAIEAMNG-QYLCNRPITVSYAFKKDSKGSGPSS 95
>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 = 8e-06, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
++ + NL + + L + + GRV D+YIPRD+ T + +GFAFV + + A+
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
Query: 91 LFSGIVTLYNRTLRFALS 108
G V L R LR ++
Sbjct: 108 AMDGAV-LDGRELRVQMA 124
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 44.7 bits (104), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
++ + NL + + L + + GRV D+YIPRD+ T + +GFAFV + + A+
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
Query: 91 LFSGIVTLYNRTLRFALS 108
G V L R LR ++
Sbjct: 131 AMDGAV-LDGRELRVQMA 147
>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 = 43.5 bits (101), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%)
Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
G S N+Y+ NL + + L I + G +V I RDK T +P+G AFV Y E
Sbjct: 7 GGESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 66
Query: 84 IGHYAIKLFSGIV 96
AI + ++
Sbjct: 67 EAQEAISALNNVI 79
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N++I NLD+ ++ + LYD G ++ + D+ + KG+ FV +E++E AI+
Sbjct: 7 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 64
Query: 92 FSGIV 96
+G++
Sbjct: 65 MNGML 69
>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 = 43.1 bits (100), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N++I NLD+ ++ + LYD G ++ + D+ + KG+ FV +E++E AI+
Sbjct: 100 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 157
Query: 92 FSGIV 96
+G++
Sbjct: 158 MNGML 162
Score = 34.3 bits (77), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 30/49 (61%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
++Y+G+L V E +LY+ AG ++ + + RD T + G+A+V ++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 60
>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 = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N++I NLD+ ++ + LYD G ++ + D+ + KG+ FV +E++E AI+
Sbjct: 105 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 162
Query: 92 FSGIV 96
+G++
Sbjct: 163 MNGML 167
Score = 34.3 bits (77), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 15/50 (30%), Positives = 30/50 (60%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
++Y+G+L V E +LY+ AG ++ + + RD T + G+A+V ++
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQ 65
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 42.7 bits (99), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 38/65 (58%), Gaps = 2/65 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N++I NLD+ ++ + LYD G ++ + D+ + KG+ FV +E++E AI+
Sbjct: 13 NIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIEK 70
Query: 92 FSGIV 96
+G++
Sbjct: 71 MNGML 75
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 42.4 bits (98), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 28/48 (58%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
+++G LD + L Q G VVD I +DK T++ +GF FV+++
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 41.6 bits (96), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/65 (30%), Positives = 31/65 (47%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
+ + NL E E L ++ G + +Y+ +DK T + KGFAF+ + E AI
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIA 75
Query: 91 LFSGI 95
SG
Sbjct: 76 GVSGF 80
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 41.2 bits (95), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 36/78 (46%), Gaps = 1/78 (1%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
+ + NL + + L + + GRV D+YIPR+ T P+GFAFV + A
Sbjct: 14 ITLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEA 73
Query: 91 LFSGIVTLYNRTLRFALS 108
G L R LR ++
Sbjct: 74 AMDG-AELDGRELRVQVA 90
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 40.8 bits (94), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
+SGC ++IG L + + L + Q G V + + RD T + +GF FV +
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 40.4 bits (93), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 44/78 (56%), Gaps = 1/78 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+++G L NE+ L + + G++ ++ + +D+ET + +GF FV +E+ + A+
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 93 SGIVTLYNRTLRFALSGQ 110
+G ++ R +R +G+
Sbjct: 75 NG-KSVDGRQIRVDQAGK 91
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C +Y+GNL E +Y++ ++G + + + DK GF FVEY S A++
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMR 99
Query: 91 LFSGIVTLYNRTLR 104
+G L +R +R
Sbjct: 100 YING-TRLDDRIIR 112
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
VY+G++ E + D+ G V++L + D +T + KG+AF+E+ E A++
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 93 SGIVTLYNRTLRFALSGQDKNAQNSSMT 120
+G Y RF G N+ S ++
Sbjct: 66 NG----YQLGSRFLKCGYSSNSDISGVS 89
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 53/110 (48%), Gaps = 3/110 (2%)
Query: 11 PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
P VSR Q G + +++G + E E L D Q G++ + I D+ + K
Sbjct: 85 PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 143
Query: 71 PKGFAFVEYESEE-IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSM 119
+GFAFV ++ + + I+ + V +N +R ALS Q+ + +SS
Sbjct: 144 KRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQEMASASSSQ 192
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L + + L Q G + D + RD T + +GF FV Y + E
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 65
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 40/82 (48%), Gaps = 4/82 (4%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
VY+G++ E + D+ G V++L + D +T + KG+AF+E+ E A++
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 93 SGIVTLYNRTLRFALSGQDKNA 114
+G Y RF G N+
Sbjct: 67 NG----YQLGSRFLKCGYSSNS 84
>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 = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/109 (28%), Positives = 53/109 (48%), Gaps = 3/109 (2%)
Query: 11 PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
P VSR Q G + +++G + E E L D Q G++ + I D+ + K
Sbjct: 86 PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 144
Query: 71 PKGFAFVEYESEE-IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSS 118
+GFAFV ++ + + I+ + V +N +R ALS Q+ + +SS
Sbjct: 145 KRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQEMASASSS 192
Score = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L + + L Q G + D + RD T + +GF FV Y + E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 31/110 (28%), Positives = 53/110 (48%), Gaps = 3/110 (2%)
Query: 11 PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
P VSR Q G + +++G + E E L D Q G++ + I D+ + K
Sbjct: 87 PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 145
Query: 71 PKGFAFVEYESEE-IGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQNSSM 119
+GFAFV ++ + + I+ + V +N +R ALS Q+ + +SS
Sbjct: 146 KRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQEMASASSSQ 194
Score = 33.1 bits (74), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L + + L Q G + D + RD T + +GF FV Y + E
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 67
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 52/95 (54%), Gaps = 3/95 (3%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
++IG L+ + NE++L + + G + ++ + +D+ T K +GFAF+ +E+ A K
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNAAKDM 68
Query: 93 SGIVTLYNRTLRFALSGQDKNAQNSSMTTTPLSSR 127
+G +L+ + ++ + + + Q+ P SSR
Sbjct: 69 NG-KSLHGKAIKVEQA-KKPSFQSGGRRRPPASSR 101
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 1/76 (1%)
Query: 29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
S N+ + L + + +R LY + G + I RD +T G+AFV++ SE A
Sbjct: 2 SNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRA 61
Query: 89 IKLFSGIVTLYNRTLR 104
IK+ +GI T+ N+ L+
Sbjct: 62 IKVLNGI-TVRNKRLK 76
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 39/74 (52%), Gaps = 2/74 (2%)
Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
G V++ NLD KV + L ++ AG VV I DK+ K +G V +E AI
Sbjct: 15 GSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDG-KSRGIGTVTFEQSIEAVQAI 73
Query: 90 KLFSGIVTLYNRTL 103
+F+G + L++R +
Sbjct: 74 SMFNGQL-LFDRPM 86
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir
In The Complex With Fbp Nbox Peptide
Length = 199
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C VY+G++ ++ E + G + + + D T K KGFAFVEYE E A++
Sbjct: 14 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
Query: 91 LFSGIV 96
+ ++
Sbjct: 74 QMNSVM 79
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 30/57 (52%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
+Y+ ++ + +++ + + G++ + RD T K KG+ F+EYE + A+
Sbjct: 113 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 169
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 39.3 bits (90), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 4/88 (4%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
VY+G++ E + D+ G V++L + D +T + KG+AF+E+ E A++
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 93 SGIVTLYNRTLRFALSGQDKNAQNSSMT 120
+G Y RF G N+ S ++
Sbjct: 65 NG----YQLGSRFLKCGYSSNSDISGVS 88
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 34/66 (51%)
Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
GCN++I +L ++ + L + G V+ + DK+T K F FV +++ + AI
Sbjct: 40 GCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAI 99
Query: 90 KLFSGI 95
K +G
Sbjct: 100 KAMNGF 105
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/79 (24%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
S+ +Y+G+L + E +L I G++ ++ + +D +T + KG+ F+ + E
Sbjct: 1 GSSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECA 60
Query: 86 HYAIKLFSGIVTLYNRTLR 104
A++ +G L R +R
Sbjct: 61 RRALEQLNGF-ELAGRPMR 78
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 31/55 (56%)
Query: 29 SGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
S VY+ NL + LY I + G+VV + I +DK+T K KG AF+ + ++
Sbjct: 15 SKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKD 69
>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 = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C VY+G++ ++ E + G + + D T K KGFAFVEYE E A++
Sbjct: 13 CRVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
Score = 32.0 bits (71), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 30/57 (52%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
+Y+ ++ + +++ + + G++ + RD T K KG+ F+EYE + A+
Sbjct: 112 IYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAV 168
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%)
Query: 42 VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG 94
V ++ L + +AG+VV++ P D+ T K KGF FVE S IK F G
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 32/63 (50%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+Y+G+L + E +L I GR+ + + D ET + KG+ F+ + E A++
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQL 88
Query: 93 SGI 95
+G
Sbjct: 89 NGF 91
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 29/53 (54%)
Query: 42 VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSG 94
V ++ L + +AG+VV++ P D+ T K KGF FVE S IK F G
Sbjct: 24 VLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIKSFHG 76
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 37.7 bits (86), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 33/72 (45%), Gaps = 12/72 (16%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRV----------VDLYIPRDKETDKPKGFAFVEYESE 82
+Y+ L++ V L D Q G V + +Y+ DKET KPKG A V YE
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKETGKPKGDATVSYEDP 75
Query: 83 EIGHYAIKLFSG 94
A++ F G
Sbjct: 76 PTAKAAVEWFDG 87
>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 = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 29/102 (28%), Positives = 49/102 (48%), Gaps = 3/102 (2%)
Query: 11 PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
P VSR Q G + +++G + E E L D Q G++ + I D+ + K
Sbjct: 79 PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 137
Query: 71 PKGFAFVEYESEE-IGHYAIKLFSGIVTLYNRTLRFALSGQD 111
+GFAFV ++ + + I+ + V +N +R ALS Q+
Sbjct: 138 KRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQE 178
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L + + L Q G + D + RD T + +GF FV Y + E
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 59
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 3/101 (2%)
Query: 11 PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
P VSR Q G + +++G + E E L D Q G++ + I D+ + K
Sbjct: 86 PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 144
Query: 71 PKGFAFVEYESEE-IGHYAIKLFSGIVTLYNRTLRFALSGQ 110
+GFAFV ++ + + I+ + V +N +R ALS Q
Sbjct: 145 KRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQ 184
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L + + L Q G + D + RD T + +GF FV Y + E
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 66
>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 = 37.0 bits (84), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 32/65 (49%)
Query: 19 KRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVE 78
KR I + +++G + V + + Q G ++D + DK+T + +GF FV
Sbjct: 76 KRAIPRDEQDKTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVT 135
Query: 79 YESEE 83
Y+S +
Sbjct: 136 YDSAD 140
Score = 37.0 bits (84), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 17/50 (34%), Positives = 27/50 (54%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
C ++IG L+ E L + + G V DL I +D T + +GF F+ +E
Sbjct: 4 CKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFE 53
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 3/101 (2%)
Query: 11 PNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK 70
P VSR Q G + +++G + E E L D Q G++ + I D+ + K
Sbjct: 84 PKRAVSREDSQ-RPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGK 142
Query: 71 PKGFAFVEYESEE-IGHYAIKLFSGIVTLYNRTLRFALSGQ 110
+GFAFV ++ + + I+ + V +N +R ALS Q
Sbjct: 143 KRGFAFVTFDDHDSVDKIVIQKYH-TVNGHNCEVRKALSKQ 182
Score = 32.3 bits (72), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/52 (30%), Positives = 25/52 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L + + L Q G + D + RD T + +GF FV Y + E
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVE 64
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 37.0 bits (84), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 29/111 (26%), Positives = 52/111 (46%), Gaps = 4/111 (3%)
Query: 1 LVPSPKH--SFVPNDVVSRNKRQIMS-GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRV 57
LVP H S + R R + + N + C + + L ER L ++ + G +
Sbjct: 14 LVPRGSHMASMTGGQQMGRGSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPI 73
Query: 58 VDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
D+ I D+++ + +GFAFV +E+ + A + +G+ L R +R S
Sbjct: 74 ADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGM-ELDGRRIRVDFS 123
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 46/102 (45%), Gaps = 3/102 (2%)
Query: 24 SGNSNSGCNVYIGNLDE-KVNERVLYDILIQAGRVVDLYI-PRDKETDKPKGFAFVEYES 81
S S+ C ++IG + + K E +L +I V+D+ + + K +GFAFVEYES
Sbjct: 2 SSGSSGNCRLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYES 61
Query: 82 EEIGHYA-IKLFSGIVTLYNRTLRFALSGQDKNAQNSSMTTT 122
A KL G + L+ + + + + M T
Sbjct: 62 HRAAAMARRKLMPGRIQLWGHQIAVDWAEPEIDVDEDVMETV 103
>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 = 36.2 bits (82), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C +Y+GNL E +Y++ ++G + + + DK GF FVEY S A++
Sbjct: 19 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAENAMR 77
Query: 91 LFSGIVTLYNRTLR 104
+G L +R +R
Sbjct: 78 YING-TRLDDRIIR 90
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.8 bits (81), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+Y+GNLD+ + E +L G + ++ I DK +K +AFVEY + A++
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 93 SG 94
+G
Sbjct: 62 NG 63
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/86 (20%), Positives = 41/86 (47%), Gaps = 1/86 (1%)
Query: 10 VPNDVVSRNKR-QIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKET 68
+ N++V N Q +S+ N+++G+L+ V++ L + + ++ D +T
Sbjct: 66 IENNIVKINWAFQSQQSSSDDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQT 125
Query: 69 DKPKGFAFVEYESEEIGHYAIKLFSG 94
+G+ FV + S++ A+ G
Sbjct: 126 GSSRGYGFVSFTSQDDAQNAMDSMQG 151
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug
Triplet Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 35/66 (53%)
Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
G N++I +L ++ ++ L + + G VV + DK+T+ K F FV Y++ AI
Sbjct: 25 GANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAAI 84
Query: 90 KLFSGI 95
+ +G
Sbjct: 85 QSMNGF 90
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 35.8 bits (81), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 2/76 (2%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
++I L + L +I G V DL + ++ KPKG A+VEYE+E A+
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNR-AGKPKGLAYVEYENESQASQAVMKM 78
Query: 93 SGIVTLYNRTLRFALS 108
G+ T+ ++ A+S
Sbjct: 79 DGM-TIKENIIKVAIS 93
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 35.8 bits (81), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 8/72 (11%)
Query: 10 VPNDVVSRNKRQIMSGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETD 69
VP + R K Q ++IG L + E L + Q G++ D + RD +
Sbjct: 15 VPLERKKREKEQFR--------KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASK 66
Query: 70 KPKGFAFVEYES 81
+ +GF FV + S
Sbjct: 67 RSRGFGFVTFSS 78
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 9/90 (10%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C +++GNL + E + + G +++I RD +GF F+ ES + A
Sbjct: 23 CRLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD------RGFGFIRLESRTLAEIAKA 76
Query: 91 LFSGIVTLYNRTL--RFALSGQDKNAQNSS 118
G + L +R L RFA G +N S
Sbjct: 77 ELDGTI-LKSRPLRIRFATHGAALTVKNLS 105
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.8 bits (81), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C VY+GNL N+ L G + +++ R+ P GFAFVE+E A++
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 128
Query: 91 LFSGIVTLYNRTLRFALSGQDK 112
G TL +R LS +K
Sbjct: 129 ELDG-RTLCGCRVRVELSNGEK 149
>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 = 35.8 bits (81), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%), Gaps = 1/72 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
VY+G++ ++ E + G + + + D T K KGFAFVEYE E A++
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 93 SGIVTLYNRTLR 104
+ ++ L R ++
Sbjct: 91 NSVM-LGGRNIK 101
Score = 32.3 bits (72), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 13/57 (22%), Positives = 30/57 (52%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
+Y+ ++ + +++ + + G++ + RD T K KG+ F+EYE + A+
Sbjct: 128 IYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAV 184
>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 = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
V++G+L ++ + GR+ D + +D T K KG+ FV + ++ AI+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 93 SGIVTLYNRTLR 104
G L R +R
Sbjct: 78 GG-QWLGGRQIR 88
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.4 bits (80), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 26/82 (31%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
C VY+GNL N+ L G + +++ R+ P GFAFVE+E A++
Sbjct: 74 CKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARN-----PPGFAFVEFEDPRDAADAVR 128
Query: 91 LFSGIVTLYNRTLRFALSGQDK 112
G TL +R LS +K
Sbjct: 129 DLDG-RTLCGCRVRVELSNGEK 149
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 15/49 (30%), Positives = 25/49 (51%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
C ++IG L + + L + Q G V + + RD T + +GF FV +
Sbjct: 1 CKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
N+YI L + ++ + D+ + GR+++ + D+ T +G AF+ ++ AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 91 LFSG 94
F+G
Sbjct: 149 SFNG 152
>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 = 35.4 bits (80), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
N+YI L + ++ + D+ + GR+++ + D+ T +G AF+ ++ AI
Sbjct: 89 ANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 91 LFSG 94
F+G
Sbjct: 149 SFNG 152
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 35.0 bits (79), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 3/63 (4%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
+++ NL +E L + G + +L+ P D T KPKGFAFV + E +A+K +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE---HAVKAY 67
Query: 93 SGI 95
+ +
Sbjct: 68 AEV 70
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 34.7 bits (78), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 7/58 (12%)
Query: 30 GCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKP-KGFAFVEYESEEIGH 86
G V++G E + L Q G VVD++IP KP + FAFV + +++
Sbjct: 11 GSKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIP------KPFRAFAFVTFADDKVAQ 62
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 34.7 bits (78), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 29/92 (31%), Positives = 48/92 (52%), Gaps = 14/92 (15%)
Query: 33 VYIGNLD----EKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
Y+GNL + + + D+ I++ R+V RDK+TDK KGF +VE+ +E+
Sbjct: 18 AYVGNLPFNTVQGDIDAIFKDLSIRSVRLV-----RDKDTDKFKGFCYVEF--DEVDSLK 70
Query: 89 IKLFSGIVTLYNRTLRFALS---GQDKNAQNS 117
L L +R+LR ++ QDK+ +S
Sbjct: 71 EALTYDGALLGDRSLRVDIAEGRKQDKSGPSS 102
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 34.7 bits (78), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 40/77 (51%), Gaps = 1/77 (1%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N+ + + V+E L + + G + + I D+ET + +G+ FV+++S AI
Sbjct: 44 NLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 92 FSGIVTLYNRTLRFALS 108
+G + N+ L+ AL+
Sbjct: 104 LNGF-NILNKRLKVALA 119
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 34.3 bits (77), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 22/32 (68%)
Query: 53 QAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
Q G+V D + DK T++ +GF FV +ESE+I
Sbjct: 22 QFGKVDDAMLMFDKTTNRHRGFGFVTFESEDI 53
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 34.3 bits (77), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 33/66 (50%), Gaps = 6/66 (9%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE-----IGH 86
N+YI NL ++E+ L ++L G+V+ I RD + +G F ES E IGH
Sbjct: 27 NLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVGFARMESTEKCEAVIGH 85
Query: 87 YAIKLF 92
+ K
Sbjct: 86 FNGKFI 91
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 33.9 bits (76), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 30/60 (50%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
+++G + E L + + G V ++ + D E +P+GF F+ +E E+ A+ +
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNM 71
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 33.9 bits (76), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 22/83 (26%), Positives = 42/83 (50%), Gaps = 1/83 (1%)
Query: 26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
N + C + + L ER L ++ + G + D+ I D+++ + +GFAFV +E+ +
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 86 HYAIKLFSGIVTLYNRTLRFALS 108
A + +G+ L R +R S
Sbjct: 71 KEAKERANGM-ELDGRRIRVDFS 92
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 33.9 bits (76), Expect = 0.071, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 25 GNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
N + C + + L ER L ++ + G + D+ I D+++ + +GFAFV +E+ +
Sbjct: 7 ANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDD 66
Query: 85 GHYAIKLFSGIVTLYNRTLRFALS 108
A + +G+ L R +R S
Sbjct: 67 AKEAKERANGM-ELDGRRIRVDFS 89
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 28/58 (48%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
+YI L ++ L + G++V DK T+K KG+ FV+++S A+
Sbjct: 7 GLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of
Hypothetical Polyadenylate-Binding Protein (Pabpn1)
From Homo Sapiens At 1.95 A Resolution
Length = 89
Score = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++Y+GN+D L G V + I DK + PKGFA++E+ +E
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 59
>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 = 33.1 bits (74), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 27/57 (47%)
Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYE 80
S N ++G L +++ L D + G VVD I D T + +GF F+ ++
Sbjct: 5 SKNEEDAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFK 61
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIG 85
N + C + + L ER L ++ + G + D+ I D+++ + +GFAFV +E+ +
Sbjct: 11 NPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDA 70
Query: 86 HYAIKLFSGIVTLYNRTLR 104
A + +G+ L R +R
Sbjct: 71 KEAKERANGM-ELDGRRIR 88
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 31/55 (56%), Gaps = 3/55 (5%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
N+ C +Y+GNL + + + D+ + G + D+ + +++ P FAFVE+E
Sbjct: 19 GNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFED 70
>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 = 32.7 bits (73), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++Y+GN+D L G V + I DK + PKGFA++E+ +E
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58
>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 = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ + E+ E ++D + G + ++++ D+ T KG+ VEYE+ +
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 87 YAIKLFSG 94
A++ +G
Sbjct: 64 AAMEGLNG 71
>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 = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ + E+ E ++D + G + ++++ D+ T KG+ VEYE+ +
Sbjct: 6 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 65
Query: 87 YAIKLFSG 94
A++ +G
Sbjct: 66 AAMEGLNG 73
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 32.3 bits (72), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/91 (24%), Positives = 46/91 (50%), Gaps = 12/91 (13%)
Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQ------AGRVVDLYIPRDKETDKPKGFAFV 77
SG+S ++++G+L V++ +LY+ ++ G+VV +T KG+ FV
Sbjct: 3 SGSSGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVV------LDQTGVSKGYGFV 56
Query: 78 EYESEEIGHYAIKLFSGIVTLYNRTLRFALS 108
++ E A+ G V L ++ +R +++
Sbjct: 57 KFTDELEQKRALTECQGAVGLGSKPVRLSVA 87
>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 = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ + E+ E ++D + G + ++++ D+ T KG+ VEYE+ +
Sbjct: 20 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 79
Query: 87 YAIKLFSG 94
A++ +G
Sbjct: 80 AAMEGLNG 87
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ + E+ E ++D + G + ++++ D+ T KG+ VEYE+ +
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 87 YAIKLFSG 94
A++ +G
Sbjct: 64 AAMEGLNG 71
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 24/47 (51%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
V++G+L ++ + G++ D + +D T K KG+ FV +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 32.3 bits (72), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 32/64 (50%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
N+Y+ L + ++++ + + Q GR++ I D+ T +G F+ ++ AIK
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 91 LFSG 94
+G
Sbjct: 151 GLNG 154
>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 = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ + E+ E ++D + G + ++++ D+ T KG+ VEYE+ +
Sbjct: 4 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 63
Query: 87 YAIKLFSG 94
A++ +G
Sbjct: 64 AAMEGLNG 71
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 32/64 (50%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
N+Y+ L + ++++ + + Q GR++ I D+ T +G F+ ++ AIK
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 61
Query: 91 LFSG 94
+G
Sbjct: 62 GLNG 65
>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 = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG L ++ L D + G VVD + D T + +GF FV ++ E
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESE 52
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 29/72 (40%), Gaps = 3/72 (4%)
Query: 26 NSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDK---PKGFAFVEYESE 82
S+ ++I NL+ E L + + G + I + K GF FVEY+
Sbjct: 1 GSSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKP 60
Query: 83 EIGHYAIKLFSG 94
E A+K G
Sbjct: 61 EQAQKALKQLQG 72
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain
Of Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 32.0 bits (71), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
+++G L E + + G V + +P D +T+K +GF F+ ++ EE
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 54
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
V+ L ++ R L D G+V D+ I D+ + + KG A+VE+
Sbjct: 27 TVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEF 74
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 7/56 (12%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKP-KGFAFVEYESEEIGH 86
V++G + E L + Q G V+D++IP KP + FAFV + ++I
Sbjct: 7 GVFVGRCTGDMTEDELREFFSQYGDVMDVFIP------KPFRAFAFVTFADDQIAQ 56
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 14/51 (27%), Positives = 27/51 (52%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
+++G L E + + G V + +P D +T+K +GF F+ ++ EE
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEE 52
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 32.0 bits (71), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 13/48 (27%), Positives = 28/48 (58%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
+++G + ++E+ L + + GR+ +L + +D+ T KG AF+ Y
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTY 64
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 32.0 bits (71), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 31/64 (48%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIK 90
N+Y+ L + + ++ L + Q GR++ I D+ T +G F+ ++ AIK
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 91 LFSG 94
+G
Sbjct: 149 GLNG 152
>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 = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 36/68 (52%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ + E+ E ++D + G + ++++ D+ T KG+ VEYE+ +
Sbjct: 19 SVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQ 78
Query: 87 YAIKLFSG 94
A++ +G
Sbjct: 79 AAMEGLNG 86
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 31.6 bits (70), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 29/52 (55%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
++IG + ++E+ L + + G++ +L + +D+ T KG AF+ Y E
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERE 66
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 31.6 bits (70), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 33/68 (48%)
Query: 28 NSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHY 87
+S ++IG L +N+ + ++L G + + +D T KG+AF EY +
Sbjct: 112 DSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 88 AIKLFSGI 95
AI +G+
Sbjct: 172 AIAGLNGM 179
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 31.6 bits (70), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 9/92 (9%)
Query: 24 SGNSNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEE 83
SG+S + +++GN+ + L + + GRV++ + +D +AFV E E
Sbjct: 3 SGSSGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD--------YAFVHMEKEA 54
Query: 84 IGHYAIKLFSGIVTLYNRT-LRFALSGQDKNA 114
AI +G R + + GQ K+
Sbjct: 55 DAKAAIAQLNGKEVKGKRINVELSTKGQKKSG 86
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 31.6 bits (70), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 31/71 (43%), Gaps = 5/71 (7%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
VY+GNL + L G + ++I R+ P GFAFVE+E A++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN-----PPGFAFVEFEDPRDAEDAVRG 56
Query: 92 FSGIVTLYNRT 102
G V +R
Sbjct: 57 LDGKVICGSRV 67
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 31.6 bits (70), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 30/59 (50%), Gaps = 9/59 (15%)
Query: 33 VYIGNLDEKVNERVL---YDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
+++ L E E L +D ++A R+V D+ET KGF FV++ SEE A
Sbjct: 18 LFVKGLSEDTTEETLKESFDGSVRA-RIV-----TDRETGSSKGFGFVDFNSEEDAKAA 70
>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 = 31.2 bits (69), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEY 79
+VY+GN+D + L G + + I DK + PKG+A++E+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEF 85
>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 = 31.2 bits (69), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 20/38 (52%)
Query: 66 KETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTL 103
K + KP+G+AF+EYE E H A K G R L
Sbjct: 138 KRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVL 175
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 31.2 bits (69), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 36/79 (45%), Gaps = 7/79 (8%)
Query: 26 NSNSGCN-VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEI 84
+ +SG N +YIGNL V L + D +P + G+AFV+Y +
Sbjct: 3 SGSSGMNKLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNW 56
Query: 85 GHYAIKLFSGIVTLYNRTL 103
AI+ SG V L+ + +
Sbjct: 57 AIRAIETLSGKVELHGKIM 75
>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 = 30.8 bits (68), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 14/29 (48%), Positives = 18/29 (62%)
Query: 66 KETDKPKGFAFVEYESEEIGHYAIKLFSG 94
K + KP+G+AF+EYE E H A K G
Sbjct: 138 KRSGKPRGYAFIEYEHERDMHSAYKHADG 166
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 30.8 bits (68), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
++IG L +N+ + ++L G + + +D T KG+AF EY + AI
Sbjct: 99 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 158
Query: 93 SGI 95
+G+
Sbjct: 159 NGM 161
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
++IG L +N+ + ++L G + + +D T KG+AF EY + AI
Sbjct: 97 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 156
Query: 93 SGI 95
+G+
Sbjct: 157 NGM 159
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 35/73 (47%), Gaps = 1/73 (1%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
+V++G+L ++ + GR+ D + +D T K KG+ FV + ++ AI+
Sbjct: 8 HVFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 67
Query: 92 FSGIVTLYNRTLR 104
G L R +R
Sbjct: 68 MGG-QWLGGRQIR 79
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 30.4 bits (67), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 14/55 (25%), Positives = 30/55 (54%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYES 81
S G +++ ++ E+ E + + G + ++++ D+ T KG+A VEYE+
Sbjct: 23 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYET 77
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 30.0 bits (66), Expect = 0.90, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 31/63 (49%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLF 92
++IG L +N+ + ++L G + + +D T KG+AF EY + AI
Sbjct: 4 LFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGL 63
Query: 93 SGI 95
+G+
Sbjct: 64 NGM 66
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 30.0 bits (66), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 33 VYIGNLDEK-VNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
V+IGNL+ V + + I + GRV + KG+AFV+Y +E A+
Sbjct: 30 VFIGNLNTALVKKSDVETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAVLG 81
Query: 92 FSGIVTLYNRTLRFALSGQDK 112
+G V L +TL ++G+ K
Sbjct: 82 ENGRV-LAGQTLDINMAGEPK 101
>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 = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/68 (23%), Positives = 35/68 (51%)
Query: 27 SNSGCNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGH 86
S G +++ ++ E+ E + + G + ++++ D+ T KG+A VEYE+ +
Sbjct: 69 SVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQAL 128
Query: 87 YAIKLFSG 94
A + +G
Sbjct: 129 AAKEALNG 136
>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 = 29.6 bits (65), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
+++GNL + E + + + G+ +++I +D KGF F+ E+ + A
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA 67
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/63 (20%), Positives = 31/63 (49%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N+++G+L+ V++ L + + ++ D +T +G+ FV + S++ A+
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDS 62
Query: 92 FSG 94
G
Sbjct: 63 MQG 65
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.9 bits (63), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 40/85 (47%), Gaps = 3/85 (3%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAIKL 91
N+Y+ NLD+ +++ L G + + E + KGF FV + S E A+
Sbjct: 17 NLYVKNLDDGIDDERLRKAFSPFGTITSAKVM--MEGGRSKGFGFVCFSSPEEATKAVTE 74
Query: 92 FSGIVTLYNRTLRFALSGQDKNAQN 116
+G + + + L AL+ + + Q+
Sbjct: 75 MNGRI-VATKPLYVALAQRKEERQS 98
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 6/56 (10%)
Query: 33 VYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYA 88
+++GNL + E + + + G+ +++I +D KGF F+ E+ + A
Sbjct: 25 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIA 74
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 28.5 bits (62), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDKETDKPKGFAFVEYESEEIGHYAI 89
C VY G + + ++++ G+++++ + + KG++FV + + E +AI
Sbjct: 26 CTVYCGGIASGLTDQLMRQTFSPFGQIMEIRVFPE------KGYSFVRFSTHESAAHAI 78
>pdb|2DIV|A Chain A, Solution Structure Of The Rrm Domain Of Trna
Selenocysteine Associated Protein
Length = 99
Score = 28.5 bits (62), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 32 NVYIGNLDEKVNERVLYDILIQAGR-VVDLYIPRDKETDKPKGFAFVEY 79
++++G+L+ ++E + G V+ + I R++ T P G+ FVE+
Sbjct: 11 SLWMGDLEPYMDENFISRAFATMGETVMSVKIIRNRLTGIPAGYCFVEF 59
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.1 bits (61), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 33/65 (50%), Gaps = 1/65 (1%)
Query: 31 CNVYIGNLDEKVNERVLYDILIQAGRVVDLYIPRDK-ETDKPKGFAFVEYESEEIGHYAI 89
V+IG L V + + +I G++ + +P ++ KG+A+VE+E+ + A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 90 KLFSG 94
K G
Sbjct: 65 KHMDG 69
>pdb|3KGX|A Chain A, Crystal Structure Of Putative Aminotransferase
(Aah25799.1) From Mus Musculus At 1.80 A Resolution
pdb|3KGX|B Chain B, Crystal Structure Of Putative Aminotransferase
(Aah25799.1) From Mus Musculus At 1.80 A Resolution
pdb|3KGW|A Chain A, Crystal Structure Of Putative Aminotransferase
(Aah25799.1) From Mus Musculus At 1.65 A Resolution
pdb|3KGW|B Chain B, Crystal Structure Of Putative Aminotransferase
(Aah25799.1) From Mus Musculus At 1.65 A Resolution
Length = 393
Score = 26.9 bits (58), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/58 (22%), Positives = 27/58 (46%)
Query: 59 DLYIPRDKETDKPKGFAFVEYESEEIGHYAIKLFSGIVTLYNRTLRFALSGQDKNAQN 116
++ +P P G+ + + S + H++I++ G+ R LR L G + +N
Sbjct: 316 EIRLPTITTVTVPAGYNWRDIVSYVLDHFSIEISGGLGPTEERVLRIGLLGYNATTEN 373
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
0.314 0.131 0.379
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,628,729
Number of Sequences: 62578
Number of extensions: 274665
Number of successful extensions: 550
Number of sequences better than 100.0: 132
Number of HSP's better than 100.0 without gapping: 107
Number of HSP's successfully gapped in prelim test: 25
Number of HSP's that attempted gapping in prelim test: 415
Number of HSP's gapped (non-prelim): 151
length of query: 211
length of database: 14,973,337
effective HSP length: 95
effective length of query: 116
effective length of database: 9,028,427
effective search space: 1047297532
effective search space used: 1047297532
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)