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= psy3928
(115 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 45.8 bits (107), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPK-FKSTGKLKGFAFVEFSTKEEATKALE 72
+L +P +A I +FS +G++ V LPK TG +GF FV+F TK++A KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 45.4 bits (106), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
LP D ++++F KYG + ++ + K TG+ +G AFV ++ +EEA +A+ N
Sbjct: 96 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 155
Query: 79 P 79
P
Sbjct: 156 P 156
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 30/54 (55%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP + + ++F G + + + TG G+AFV+F+++ ++ +A+++
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
>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 = 45.1 bits (105), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 35/61 (57%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
LP D ++++F KYG + ++ + K TG+ +G AFV ++ +EEA +A+ N
Sbjct: 107 NLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVI 166
Query: 79 P 79
P
Sbjct: 167 P 167
Score = 28.5 bits (62), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 30/54 (55%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP + + ++F G + + + TG G+AFV+F+++ ++ +A+++
Sbjct: 22 LPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKV 75
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 35/60 (58%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCP 79
LP D ++++F KYG + ++ + K TG+ +G AFV ++ +EEA +A+ N P
Sbjct: 21 LPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIP 80
>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 = 45.1 bits (105), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/60 (38%), Positives = 35/60 (58%), Gaps = 1/60 (1%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYG-KVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+V+ LP A D I +G + V L + KS+G+ +GFAFVEFS ++AT+ +E
Sbjct: 3 IVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRWME 62
>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 = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 29/46 (63%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
D + VF KYG+V V +P+ + T + +GFAFV F K +A A++
Sbjct: 62 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 107
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 43.5 bits (101), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 19/46 (41%), Positives = 29/46 (63%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
D + VF KYG+V V +P+ + T + +GFAFV F K +A A++
Sbjct: 85 DTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMD 130
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 20/47 (42%), Positives = 30/47 (63%), Gaps = 1/47 (2%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKL-KGFAFVEFSTKEEATKALE 72
D+I +FS YGK+ + +P + L KG+A+VEF +EA KAL+
Sbjct: 19 DHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 42.4 bits (98), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 30/43 (69%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
++ +F +G ++ + L K K+TG+ KGFAF+ F +E+A +A+
Sbjct: 32 LQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 42.0 bits (97), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
D + +F +GK+ + L K TG+ KG+ F+ FS E A +ALE
Sbjct: 20 DMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
>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 = 41.6 bits (96), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G ++ + EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 72 ELGLN 76
E GLN
Sbjct: 67 E-GLN 70
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
Length = 89
Score = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G ++ + EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 66
Query: 72 ELGLN 76
E GLN
Sbjct: 67 E-GLN 70
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 37/65 (56%), Gaps = 1/65 (1%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G ++ + EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 72 ELGLN 76
E GLN
Sbjct: 82 E-GLN 85
>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 = 41.2 bits (95), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+E GLN
Sbjct: 34 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 86
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+E GLN
Sbjct: 18 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 70
>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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/54 (40%), Positives = 33/54 (61%), Gaps = 1/54 (1%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
EA + I F++YG++ + L + TG LKG+ VE+ T +EA A+E GLN
Sbjct: 20 EATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAME-GLN 72
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 32/53 (60%), Gaps = 1/53 (1%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPCPTD 81
+E VFSKYG+++ V + K + T + +GF FV F ++A A+ + +N D
Sbjct: 29 LEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAM-MAMNGKSVD 80
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ L E + + + F +G +T + +P T K +GFAFVEF E+A A++
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ L E + + + F +G +T + +P T K +GFAFVEF E+A A++
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
>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 = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 3 ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
+L E + + R+ + + + D I+SVF +GK+ +L + +TGK KG+ F+E+
Sbjct: 117 QLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYE 175
Query: 63 TKEEATKAL 71
+ + A+
Sbjct: 176 KAQSSQDAV 184
Score = 34.3 bits (77), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 25/50 (50%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
E D I F+ +G + + + T K KGFAFVE+ E A ALE
Sbjct: 39 ELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 88
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ L E + + + F +G +T + +P T K +GFAFVEF E+A A++
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ L E + + + F +G +T + +P T K +GFAFVEF E+A A++
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 32/60 (53%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RV+ L E + + + F +G +T + +P T K +GFAFVEF E+A A++
Sbjct: 6 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 65
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 40.4 bits (93), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 1 MAELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVE 60
+ +L E + + R+ + + + D I+SVF +GK+ +L + +TGK KG+ F+E
Sbjct: 99 IDQLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIE 157
Query: 61 FSTKEEATKAL 71
+ + + A+
Sbjct: 158 YEKAQSSQDAV 168
Score = 33.1 bits (74), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 24/50 (48%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
E D I F+ +G + + T K KGFAFVE+ E A ALE
Sbjct: 23 ELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALE 72
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 19/69 (27%), Positives = 38/69 (55%), Gaps = 1/69 (1%)
Query: 3 ELVENNKKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
+L E + + R+ + + + D I+SVF +GK+ +L + +TGK KG+ F+E+
Sbjct: 102 QLAEEARAFNRIYVAS-VHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEYE 160
Query: 63 TKEEATKAL 71
+ + A+
Sbjct: 161 KAQSSQDAV 169
Score = 34.3 bits (77), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 19/50 (38%), Positives = 25/50 (50%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
E D I F+ +G + + + T K KGFAFVE+ E A ALE
Sbjct: 24 ELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALE 73
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 23/56 (41%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA---TKALE 72
LP ++ + +FSKYGKV V++ K K T K KG AF+ F K+ A T+A+
Sbjct: 24 LPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAIN 79
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46
Splicing Factor
Length = 103
Score = 40.0 bits (92), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 25/44 (56%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
D + VF KYG+V V +P+ T +GFAFV F + +A A
Sbjct: 28 DSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDA 71
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 32/57 (56%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
V L PE + I+S F+ +GK++ + K +TGK KG+ FV F K +A A+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAI 74
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 17/46 (36%), Positives = 26/46 (56%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
D + +F +G++ + L TG+ KG+ F+ FS E A KALE
Sbjct: 41 DMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALE 86
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
Length = 110
Score = 38.9 bits (89), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G ++ + EA+ D I+ F YG++ + L + TG KG+A VE+ T ++A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 72 E 72
E
Sbjct: 86 E 86
>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 = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 30/53 (56%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ EA+ D I+ F YG++ + L + TG KG+A VE+ T ++A A E
Sbjct: 80 IHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKE 132
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In
Cytotoxic Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 38.5 bits (88), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
V L PE + I++ F+ +G+++ + K +TGK KG+ FV F K +A A++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 75
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
R V +P EA + ++ +FS+ G V L + TGK KG+ F E+ +E A A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
>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 = 37.7 bits (86), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 28/44 (63%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ S+FSK GKV + P ++TGK KGF FVE + +A K ++
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 72
>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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 19/44 (43%), Positives = 28/44 (63%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ S+FSK GKV + P ++TGK KGF FVE + +A K ++
Sbjct: 29 LTSLFSKAGKVVNMEFPIDEATGKTKGFLFVECGSMNDAKKIIK 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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE-----LG 74
L P+ + I F +G+V + LP T K +GF F+ F +E K +E +G
Sbjct: 9 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVG 68
Query: 75 LNPC 78
L+ C
Sbjct: 69 LSKC 72
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain
Of Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 5/64 (7%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE-----LG 74
L P+ + I F +G+V + LP T K +GF F+ F +E K +E +G
Sbjct: 7 LSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEKKYHNVG 66
Query: 75 LNPC 78
L+ C
Sbjct: 67 LSKC 70
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 36.2 bits (82), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 28/42 (66%)
Query: 32 VFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+F + G V +PK + TG+ +G+ FVEF ++E+A A+++
Sbjct: 35 LFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP +E +FS+YG++ + ++TG +G F+ F + EA +A++ GLN
Sbjct: 98 LPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK-GLN 153
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP D +S+F G + L + K TG+ G+ FV +S +A KA+
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
>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 = 0.006, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP +E +FS+YG++ + ++TG +G F+ F + EA +A++ GLN
Sbjct: 9 LPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK-GLN 64
>pdb|2LKZ|A Chain A, Solution Structure Of The Second Rrm Domain Of Rbm5
Length = 95
Score = 35.8 bits (81), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 32/61 (52%), Gaps = 2/61 (3%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
++ + P D I + S Y V + L K K T + +GFAFV+ S+ +A++ L+
Sbjct: 12 IILRNIAPHTVVDSIMTALSPYASLAVNNIRLIKDKQTQQNRGFAFVQLSSAMDASQLLQ 71
Query: 73 L 73
+
Sbjct: 72 I 72
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP +E +FS++G++ + ++TG +G AF+ F + EA +A+
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP D + S+FS G+V L + K G G+ FV + T ++A +A+
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 105 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 156
>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 = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP +E +FS++G++ + ++TG +G AF+ F + EA +A+
Sbjct: 96 LPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAI 147
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP D + S+FS G+V L + K G G+ FV + T ++A +A+
Sbjct: 10 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAI 61
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.8 bits (81), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ VFSKYG + VS+ + + + +GFAFV F ++A +A E
Sbjct: 63 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 106
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 26/53 (49%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP D +S+F G + L + K TG+ G+ FV +S +A KA+
Sbjct: 12 LPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 35.4 bits (80), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP D + S+FS G+V L + K G G+ FV + T ++A +A+
Sbjct: 12 LPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1)
From Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP D + S+FS G+V L + K G G+ FV + T ++A +A+
Sbjct: 27 LPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 113 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 164
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ VFSKYG + VS+ + + + +GFAFV F ++A +A E
Sbjct: 29 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 72
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 112 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 163
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 110 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 161
>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 = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 27/52 (51%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + E ++ F +YGK+ + + + +GK +GFAFV F + K +
Sbjct: 111 IKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIV 162
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 32/63 (50%), Gaps = 5/63 (7%)
Query: 10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
+ R +L + LP + D ++ VF ++ VS GK KG A++EF T+ +A K
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVS-----KDGKSKGIAYIEFKTEADAEK 145
Query: 70 ALE 72
E
Sbjct: 146 TFE 148
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/48 (41%), Positives = 29/48 (60%), Gaps = 1/48 (2%)
Query: 25 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
E D E VFSKYG + VS+ + + + +GFAFV F ++A +A E
Sbjct: 29 ERDLRE-VFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 17/44 (38%), Positives = 27/44 (61%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ VFSKYG + VS+ + + + +GFAFV F ++A +A E
Sbjct: 32 LREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKE 75
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 35.0 bits (79), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 3/53 (5%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LPP+ IE VF KYG + + L K + G FAFVEF +A A+
Sbjct: 29 NLPPDIRTKDIEDVFYKYGAIRDIDL-KNRRGGPP--FAFVEFEDPRDAEDAV 78
>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 = 35.0 bits (79), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP +E +FS+YG++ + + TG +G F+ F + EA +A++ GLN
Sbjct: 96 LPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK-GLN 151
Score = 30.0 bits (66), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 26/52 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP + S+F G++ L + K TG+ G+ FV + ++A KA+
Sbjct: 10 LPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAI 61
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 20/55 (36%), Positives = 33/55 (60%), Gaps = 8/55 (14%)
Query: 24 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLNPC 78
A + ++ VF K T++ +P+ GK KG+AF+EF++ E+A +A LN C
Sbjct: 27 ATEETLQEVFEK---ATFIKVPQ-NQNGKSKGYAFIEFASFEDAKEA----LNSC 73
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 34.3 bits (77), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 2/47 (4%)
Query: 25 EHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ + + FS +G +T + G+ KGF FV FS+ EEATKA+
Sbjct: 28 DDERLRKAFSPFGTITSAKV--MMEGGRSKGFGFVCFSSPEEATKAV 72
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 33.9 bits (76), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 19/48 (39%), Positives = 29/48 (60%), Gaps = 9/48 (18%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
+E++FSKYG+V S+ KG+AFV++S + A A+ LG N
Sbjct: 45 VETIFSKYGRVAGCSVH--------KGYAFVQYSNERHARAAV-LGEN 83
>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 = 0.024, Method: Compositional matrix adjust.
Identities = 19/42 (45%), Positives = 24/42 (57%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
+E +FS YG ++ + P T K KGFAFV F E A KA
Sbjct: 25 LEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKA 66
>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 = 33.9 bits (76), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+E+ F G V V++ K +G KGFA++EFS KE +L L
Sbjct: 23 LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 67
>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 = 0.025, Method: Compositional matrix adjust.
Identities = 18/45 (40%), Positives = 26/45 (57%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+E+ F G V V++ K +G KGFA++EFS KE +L L
Sbjct: 22 LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSLAL 66
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RVV +P + + I + S G V + + TG+ KG+AF+EF E + A+
Sbjct: 4 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 63
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 33.1 bits (74), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP + ++ FS +G+V V + K TG KGF FV F+ E K +
Sbjct: 23 LPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 11 YGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
+G + + L P ++ +E FS++G V + G+ G FVEF+ K A KA
Sbjct: 95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAVV-VVDDRGRATGKGFVEFAAKPPARKA 153
Query: 71 LE 72
LE
Sbjct: 154 LE 155
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RVV +P + + I + S G V + + TG+ KG+AF+EF E + A+
Sbjct: 3 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 62
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
I +FSK+GK+T P+ GK KG+ F+E+++ A A++
Sbjct: 38 IHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVK 79
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 32.7 bits (73), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 27/44 (61%), Gaps = 2/44 (4%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
I +FSK+GK+T P+ GK KG+ F+E+++ A A++
Sbjct: 24 IHKIFSKFGKITNDFYPE--EDGKTKGYIFLEYASPAHAVDAVK 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 = 32.7 bits (73), Expect = 0.048, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
RVV +P + + I + S G V + + TG+ KG+AF+EF E + A+
Sbjct: 5 RVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVR 64
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 32.7 bits (73), Expect = 0.050, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 8/43 (18%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
+E++FSKYGK+ S+ KGFAFV++ + A A+
Sbjct: 33 VEAIFSKYGKIVGCSVH--------KGFAFVQYVNERNARAAV 67
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
R ++ +P + + +F +YG + V + + T + +G+ FV+F + A +A+
Sbjct: 43 RNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIA 102
Query: 73 LGLN 76
GLN
Sbjct: 103 -GLN 105
>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 = 32.3 bits (72), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 31/58 (53%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
V L PE I + F+ +G+++ + K +TGK KG+ FV F K +A A++
Sbjct: 9 VFVGDLSPEITTAAIAAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQ 66
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 32.0 bits (71), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+V+ L + +E FS++GK+ V KLK +AF+ F ++ A KA+E
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK--------KLKDYAFIHFDERDGAVKAME 63
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 32.0 bits (71), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 31/52 (59%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
++P + ++ +F ++GK+ +++ K + TG KG AF+ + +E A KA
Sbjct: 20 QIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
>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 = 0.10, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEF 61
+ D + F KYG VT + + K +TG+ +GF F+ F
Sbjct: 14 DTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSF 52
Score = 30.0 bits (66), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 13/53 (24%), Positives = 25/53 (47%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+ P+ E FS++G + L K TG+ +GF FV + + + + +
Sbjct: 95 IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 23/36 (63%)
Query: 26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEF 61
+ + S FS+YG+V + K K+T + +GF FV+F
Sbjct: 30 QETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
LPP E + +G + L + TG+ KG+ F E+ K+ A +A
Sbjct: 102 NLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 11 YGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
+ R + ++LPP + D + S T+ L G+LKGFA +E+ T E A +
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQL-ACGQDGQLKGFAVLEYETAEMAEE 241
Query: 70 A 70
A
Sbjct: 242 A 242
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.6 bits (70), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
LPP E + +G + L + TG+ KG+ F E+ K+ A +A
Sbjct: 102 NLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 153
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 11 YGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
+ R + ++LPP + D + S T+ L G+LKGFA +E+ T E A +
Sbjct: 183 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQL-ACGQDGQLKGFAVLEYETAEMAEE 241
Query: 70 A 70
A
Sbjct: 242 A 242
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 24/52 (46%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
LPP E + +G + L + TG+ KG+ F E+ K+ A +A
Sbjct: 100 NLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARA 151
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 11 YGRVVLKEKLPPE-AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
+ R + ++LPP + D + S T+ L G+LKGFA +E+ T E A +
Sbjct: 181 HSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQL-ACGQDGQLKGFAVLEYETAEMAEE 239
Query: 70 A 70
A
Sbjct: 240 A 240
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 1/51 (1%)
Query: 21 PPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
P + D ++ + YGK+ K+T K KG+ FV+F + A KA+
Sbjct: 15 PGTTDQDLVK-LCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
E +++VF K+G ++ V L K + T K +GFAF+ F +A A
Sbjct: 18 ETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADAKNA 64
>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 = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
++ FSK+G+V +L TG+ +GF FV F E K ++
Sbjct: 16 LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 30.8 bits (68), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 5/57 (8%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFK---STGKLKGFAFVEFSTKEEATKALE 72
L PE + + FS +G + + PK TG KG+AF+ F++ + + A+E
Sbjct: 12 NLDPEIDEKLLYDTFSAFGVI--LQTPKIMRDPDTGNSKGYAFINFASFDASDAAIE 66
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
P + + + +F +G + V + L GFAFVEF E A KA+E
Sbjct: 39 FPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIE 83
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter
Pylori
Length = 90
Score = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 16/39 (41%), Positives = 23/39 (58%)
Query: 24 AEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFS 62
A + ++ +FS++GKV V L + T K KGF FVE
Sbjct: 13 ATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ 51
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
+ R +L + L D ++ VF ++ VS GK KG A++EF ++ +A K
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEK 151
Query: 70 ALE 72
LE
Sbjct: 152 NLE 154
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 30.0 bits (66), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 8/53 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
P + + + +F +G + V + L GFAFVEF E A KA+E
Sbjct: 12 FPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIE 56
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 17/49 (34%), Positives = 28/49 (57%), Gaps = 3/49 (6%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKL---KGFAFVEFSTKEEATKALE 72
+ ++ VFSK G + ++ K K+ + GF FVE+ E+A KAL+
Sbjct: 20 ETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALK 68
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.0 bits (66), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 10 KYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATK 69
+ R +L + L D ++ VF ++ VS GK KG A++EF ++ +A K
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEK 68
Query: 70 ALE 72
LE
Sbjct: 69 NLE 71
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
++ F ++GKV L K+T + +GF FV F +++ K E+
Sbjct: 16 VKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 30.0 bits (66), Expect = 0.39, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%)
Query: 9 KKYGRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAT 68
++ R V +L +E FS GKV V + +++ + KG A+VEF +
Sbjct: 22 ERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVP 81
Query: 69 KALEL 73
A+ L
Sbjct: 82 LAIGL 86
>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 = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 12/45 (26%), Positives = 26/45 (57%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
+E+ FS G + +++ K +G KG+A++EF+ + A+ +
Sbjct: 53 LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAM 97
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 29.6 bits (65), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 13/52 (25%), Positives = 31/52 (59%)
Query: 19 KLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
++P + ++ +F ++G++ +++ K + TG KG AF+ + ++ A KA
Sbjct: 22 QIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 29.6 bits (65), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP D ++ + + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 9 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 64
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 29.6 bits (65), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+V+ + L P + S+F+++ + + TG+++G AF+ F KE A +AL
Sbjct: 26 KVLYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRMMTGRMRGQAFITFPNKEIAWQALH 85
Query: 73 L 73
L
Sbjct: 86 L 86
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP D ++ + + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 102 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 157
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 29.3 bits (64), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP D ++ + + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 104 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 159
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10
From Homo Sapiens
Length = 131
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVT--YVSLPKFKSTGKLKGFAFVEFSTKEEA 67
++ L P + D I + Y ++ V + K K T +GFAF++ ST E A
Sbjct: 26 IILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQLNRGFAFIQLSTIEAA 80
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 29.3 bits (64), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELGLN 76
LP D ++ + + +G + +L K +TG KG+AF E+ +A+ GLN
Sbjct: 122 LPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA-GLN 177
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 28.9 bits (63), Expect = 0.71, Method: Compositional matrix adjust.
Identities = 12/54 (22%), Positives = 30/54 (55%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALEL 73
LP + + ++F G + + + TG G+AFV+F+++ ++ +A+++
Sbjct: 11 LPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKV 64
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 28.9 bits (63), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP EA I S+F +YGKV + +K + FV K A A+
Sbjct: 16 LPREATEQEIRSLFEQYGKVLECDI--------IKNYGFVHIEDKTAAEDAI 59
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 28.9 bits (63), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 29/60 (48%), Gaps = 8/60 (13%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
+V+ L + +E FS++GK+ V KLK +AFV F + A KA++
Sbjct: 16 KVLFVRNLATTVTEEILEKSFSEFGKLERVK--------KLKDYAFVHFEDRGAAVKAMD 67
>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 = 28.9 bits (63), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 12/44 (27%), Positives = 24/44 (54%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
++ F+K+G+V ++ +TG+ +GF F+ F K L+
Sbjct: 28 LKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLD 71
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 64
LPP+ + + +F KYGK V + K KGF F+ T+
Sbjct: 30 LPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETR 68
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
LP ++ +E FS +G+V + G+ G VEFS K A KAL+
Sbjct: 104 LPQYVSNELLEEAFSVFGQVERAVVI-VDDRGRPSGKGIVEFSGKPAARKALD 155
>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 = 28.9 bits (63), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
F YG + + + K +GK +G+AF+E+ + + A
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
>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 = 28.5 bits (62), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 64
LPP+ + + +F KYGK V + K KGF F+ T+
Sbjct: 23 LPPDITEEEMRKLFEKYGKAGEVFIH------KDKGFGFIRLETR 61
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 28.5 bits (62), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 1/52 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP I+++F + V L + K T K KGF +VEF + +AL
Sbjct: 23 LPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEAL 73
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 12/25 (48%), Positives = 18/25 (72%)
Query: 48 KSTGKLKGFAFVEFSTKEEATKALE 72
+ TG KGF FV+F+++E+A A E
Sbjct: 48 RETGSSKGFGFVDFNSEEDAKAAKE 72
>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 = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 29/52 (55%), Gaps = 1/52 (1%)
Query: 20 LPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
LP + +E + +G V + L ++ GK KG A+VE+ + +A++A+
Sbjct: 25 LPFSCTKEELEEICKAHGTVKDLRLVTNRA-GKPKGLAYVEYENESQASQAV 75
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 5/41 (12%)
Query: 27 DYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
D + FS+YG V V +PK + FAFV F+ + A
Sbjct: 20 DELREFFSQYGDVMDVFIPK-----PFRAFAFVTFADDQIA 55
>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 = 27.3 bits (59), Expect = 2.0, Method: Composition-based stats.
Identities = 11/38 (28%), Positives = 21/38 (55%)
Query: 33 FSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
F YG + + + K +GK +G+AF+E+ + + A
Sbjct: 123 FEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSA 160
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 27.3 bits (59), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G V LP +A + I + FS V V + + G++ G A VEF+T EEA A+
Sbjct: 46 GHCVHMRGLPYKATENDIYNFFSPLNPVR-VHI-EIGPDGRVTGEADVEFATHEEAVAAM 103
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGK--VTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
R V LPP+ + D I + F ++G V + + KS KG+AF+ F +E + +A
Sbjct: 9 RKVFVGGLPPDIDEDEITASFRRFGPLVVDWPHKAESKSYFPPKGYAFLLFQ-EESSVQA 67
Query: 71 L 71
L
Sbjct: 68 L 68
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 50 TGKLKGFAFVEFSTKEEATKALE 72
TG +G+ FV F+++++A A++
Sbjct: 125 TGSSRGYGFVSFTSQDDAQNAMD 147
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 26.9 bits (58), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 1/30 (3%)
Query: 42 VSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
++LP GK+ G AFV+F+++E A KAL
Sbjct: 73 ITLP-VDPEGKITGEAFVQFASQELAEKAL 101
>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 = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 8/23 (34%), Positives = 17/23 (73%)
Query: 50 TGKLKGFAFVEFSTKEEATKALE 72
TG +G+ FV F+++++A A++
Sbjct: 39 TGSSRGYGFVSFTSQDDAQNAMD 61
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleaoproteins A2B1
Length = 116
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 12/49 (24%), Positives = 27/49 (55%)
Query: 23 EAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
E + + + + ++GK+T + + ++ + +GF FV FS+ E A+
Sbjct: 38 ETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 26.9 bits (58), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 9/20 (45%), Positives = 16/20 (80%)
Query: 52 KLKGFAFVEFSTKEEATKAL 71
K++ +AFV FS +E+A +A+
Sbjct: 49 KIRDYAFVHFSNREDAVEAM 68
>pdb|2AD9|A Chain A, Solution Structure Of Polypyrimidine Tract Binding
Protein Rbd1 Complexed With Cucucu Rna
Length = 119
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAT 68
RV+ KLP + + S+ +GKVT + + K K+ AF+E +T+E A
Sbjct: 32 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ------AFIEMNTEEAAN 81
>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 = 26.9 bits (58), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G + +K L ++ + FS +G + +S KG+ FV F T+E A +A+
Sbjct: 6 GNIFIKN-LDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERAI 62
Query: 72 E 72
E
Sbjct: 63 E 63
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 26.9 bits (58), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G + +K L ++ + FS +G + +S KG+ FV F T+E A +A+
Sbjct: 12 GNIFIKN-LDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERAI 68
Query: 72 E 72
E
Sbjct: 69 E 69
>pdb|1HL6|B Chain B, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|D Chain D, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
Length = 149
Score = 26.6 bits (57), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
H+++E F GK+ Y + +K+ ++ AFV S EE + +
Sbjct: 20 HEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAFVHQSVMEELKRII 65
>pdb|1OO0|A Chain A, Crystal Structure Of The Drosophila Mago Nashi-Y14
Complex
pdb|1RK8|B Chain B, Structure Of The Cytosolic Protein Pym Bound To The
Mago- Y14 Core Of The Exon Junction Complex
pdb|2X1G|B Chain B, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|D Chain D, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 147
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 13/46 (28%), Positives = 24/46 (52%)
Query: 26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
H+++E F GK+ Y + +K+ ++ AFV S EE + +
Sbjct: 20 HEFLEFEFRPDGKLRYANNSNYKNDTMIRKEAFVHQSVMEELKRII 65
>pdb|1X4F|A Chain A, Solution Structure Of The Second Rrm Domain In Matrin 3
Length = 112
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 18/68 (26%), Positives = 31/68 (45%), Gaps = 7/68 (10%)
Query: 6 ENNKKYGRVVLKEKLPPEAEHD-YIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTK 64
+ ++ GRV+ LP D + + YGK+ L + KS AF+E T+
Sbjct: 19 DQKQELGRVIHLSNLPHSGYSDSAVLKLAEPYGKIKNYILMRMKSQ------AFIEMETR 72
Query: 65 EEATKALE 72
E+A ++
Sbjct: 73 EDAMAMVD 80
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 14 VVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKA 70
V+L + LP I+ FS++G + V LP+ T A VEF EA KA
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKA 62
>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 = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 54 KGFAFVEFSTKEEATKALE 72
KG+ FV F T+E A +A+E
Sbjct: 143 KGYGFVHFETQEAAERAIE 161
>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 = 26.2 bits (56), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G + +K L ++ + FS +G + +S KG+ FV F T+E A +A+
Sbjct: 99 GNIFIKN-LDKSIDNKALYDTFSAFGNI--LSCKVVCDENGSKGYGFVHFETQEAAERAI 155
Query: 72 E 72
E
Sbjct: 156 E 156
>pdb|1A9X|A Chain A, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
pdb|1A9X|C Chain C, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
pdb|1A9X|E Chain E, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
pdb|1A9X|G Chain G, Carbamoyl Phosphate Synthetase: Caught In The Act Of
Glutamine Hydrolysis
Length = 1073
Score = 26.2 bits (56), Expect = 4.6, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
V KE +PP + F+K+ V + P+ +STG++ G T EA +LG
Sbjct: 879 VTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVG----RTFAEAFAKAQLG 934
Query: 75 LNPCPTDYQSSILT 88
N + ++L+
Sbjct: 935 SNSTMKKHGRALLS 948
>pdb|1CE8|A Chain A, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1CE8|C Chain C, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1CE8|E Chain E, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1CE8|G Chain G, Carbamoyl Phosphate Synthetase From Escherichis Coli With
Complexed With The Allosteric Ligand Imp
pdb|1M6V|A Chain A, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
pdb|1M6V|C Chain C, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
pdb|1M6V|E Chain E, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
pdb|1M6V|G Chain G, Crystal Structure Of The G359f (Small Subunit) Point
Mutant Of Carbamoyl Phosphate Synthetase
Length = 1073
Score = 26.2 bits (56), Expect = 4.6, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
V KE +PP + F+K+ V + P+ +STG++ G T EA +LG
Sbjct: 879 VTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVG----RTFAEAFAKAQLG 934
Query: 75 LNPCPTDYQSSILT 88
N + ++L+
Sbjct: 935 SNSTMKKHGRALLS 948
>pdb|1JDB|B Chain B, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1JDB|E Chain E, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1JDB|H Chain H, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1JDB|K Chain K, Carbamoyl Phosphate Synthetase From Escherichia Coli
pdb|1BXR|A Chain A, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1BXR|C Chain C, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1BXR|E Chain E, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1BXR|G Chain G, Structure Of Carbamoyl Phosphate Synthetase Complexed With
The Atp Analog Amppnp
pdb|1C30|A Chain A, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C30|C Chain C, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C30|E Chain E, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C30|G Chain G, Crystal Structure Of Carbamoyl Phosphate Synthetase: Small
Subunit Mutation C269s
pdb|1C3O|A Chain A, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1C3O|C Chain C, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1C3O|E Chain E, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1C3O|G Chain G, Crystal Structure Of The Carbamoyl Phosphate Synthetase:
Small Subunit Mutant C269s With Bound Glutamine
pdb|1CS0|A Chain A, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1CS0|C Chain C, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1CS0|E Chain E, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1CS0|G Chain G, Crystal Structure Of Carbamoyl Phosphate Synthetase
Complexed At Cys269 In The Small Subunit With The
Tetrahedral Mimic L-glutamate Gamma-semialdehyde
pdb|1KEE|A Chain A, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1KEE|C Chain C, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1KEE|E Chain E, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1KEE|G Chain G, Inactivation Of The Amidotransferase Activity Of Carbamoyl
Phosphate Synthetase By The Antibiotic Acivicin
pdb|1T36|A Chain A, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
pdb|1T36|C Chain C, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
pdb|1T36|E Chain E, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
pdb|1T36|G Chain G, Crystal Structure Of E. Coli Carbamoyl Phosphate
Synthetase Small Subunit Mutant C248d Complexed With
Uridine 5'-Monophosphate
Length = 1073
Score = 26.2 bits (56), Expect = 4.6, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 4/74 (5%)
Query: 15 VLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALELG 74
V KE +PP + F+K+ V + P+ +STG++ G T EA +LG
Sbjct: 879 VTKEVIPPYYSVKEVVLPFNKFPGVDPLLGPEMRSTGEVMGVG----RTFAEAFAKAQLG 934
Query: 75 LNPCPTDYQSSILT 88
N + ++L+
Sbjct: 935 SNSTMKKHGRALLS 948
>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 = 26.2 bits (56), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 4/45 (8%)
Query: 29 IESVFSKYGKVTYV--SLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
I +FSK G + + L K K T GF FVE+ ++ +A A+
Sbjct: 56 IYELFSKSGDIKKIIMGLDKMKKTAC--GFCFVEYYSRADAENAM 98
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 26.2 bits (56), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 6/55 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
RV+ KLP E + ++ +GKVT + + K K+ AF+E +T+E A
Sbjct: 16 RVLHIRKLPGEVTETEVIALGLPFGKVTNILMLKGKNQ------AFLELATEEAA 64
>pdb|1NF2|A Chain A, X-Ray Crystal Structure Of Tm0651 From Thermotoga
Maritima
pdb|1NF2|B Chain B, X-Ray Crystal Structure Of Tm0651 From Thermotoga
Maritima
pdb|1NF2|C Chain C, X-Ray Crystal Structure Of Tm0651 From Thermotoga
Maritima
Length = 268
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 14 VVLKEKLPPEAEHDYIESV 32
V+L EK+PPE D IE +
Sbjct: 77 VILNEKIPPEVAKDIIEYI 95
>pdb|1SJQ|A Chain A, Nmr Structure Of Rrm1 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 105
Score = 25.8 bits (55), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 13 RVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEAT 68
RV+ KLP + + S+ +GKVT + + K K+ AF+E +T+E A
Sbjct: 17 RVIHIRKLPIDVTEGEVISLGLPFGKVTNLLMLKGKNQ------AFIEMNTEEAAN 66
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 24/44 (54%), Gaps = 8/44 (18%)
Query: 29 IESVFSKYGKVTYVSL-PKFKSTGKLKGFAFVEFSTKEEATKAL 71
+ FS +G++ + + P+ KG++FV FST E A A+
Sbjct: 42 MRQTFSPFGQIMEIRVFPE-------KGYSFVRFSTHESAAHAI 78
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 25.8 bits (55), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 26/60 (43%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
G V + LP EAE+ ++ F K V + GK G FVEF + + AL
Sbjct: 25 GFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAAL 84
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 25.8 bits (55), Expect = 7.3, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 5/39 (12%)
Query: 29 IESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEA 67
++ F +YG+V V +PK + FAFV F+ + A
Sbjct: 28 LQQFFCQYGEVVDVFIPK-----PFRAFAFVTFADDKVA 61
>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 = 25.4 bits (54), Expect = 8.5, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 5/69 (7%)
Query: 12 GRVVLKEKLPPEAEHDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKAL 71
R+++ LP + + + +F KYG + + + +T + +G A+V + +A A
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQI---RVGNTPETRGTAYVVYEDIFDAKNAC 74
Query: 72 EL--GLNPC 78
+ G N C
Sbjct: 75 DHLSGFNVC 83
>pdb|2HYI|A Chain A, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|G Chain G, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2J0Q|C Chain C, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0Q|F Chain F, The Crystal Structure Of The Exon Junction Complex At
3.2 A Resolution
pdb|2J0S|C Chain C, The Crystal Structure Of The Exon Junction Complex At
2.2 A Resolution
pdb|3EX7|A Chain A, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|E Chain E, The Crystal Structure Of Ejc In Its Transition State
pdb|2XB2|C Chain C, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
pdb|2XB2|Y Chain Y, Crystal Structure Of The Core
Mago-Y14-Eif4aiii-Barentsz- Upf3b Assembly Shows How
The Ejc Is Bridged To The Nmd Machinery
Length = 146
Score = 25.0 bits (53), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 25/47 (53%)
Query: 26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
H+++E F GK+ Y + +K+ ++ A+V S EE + ++
Sbjct: 19 HEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIID 65
>pdb|1P27|A Chain A, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|C Chain C, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 144
Score = 25.0 bits (53), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 12/47 (25%), Positives = 25/47 (53%)
Query: 26 HDYIESVFSKYGKVTYVSLPKFKSTGKLKGFAFVEFSTKEEATKALE 72
H+++E F GK+ Y + +K+ ++ A+V S EE + ++
Sbjct: 18 HEFLEFEFRPDGKLRYANNSNYKNDVMIRKEAYVHKSVMEELKRIID 64
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 0.132 0.389
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,490,825
Number of Sequences: 62578
Number of extensions: 124949
Number of successful extensions: 456
Number of sequences better than 100.0: 157
Number of HSP's better than 100.0 without gapping: 123
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 308
Number of HSP's gapped (non-prelim): 176
length of query: 115
length of database: 14,973,337
effective HSP length: 78
effective length of query: 37
effective length of database: 10,092,253
effective search space: 373413361
effective search space used: 373413361
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: 45 (21.9 bits)