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= psy10125
(312 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 97.8 bits (242), Expect = 7e-21, Method: Composition-based stats.
Identities = 44/63 (69%), Positives = 52/63 (82%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T + K ++E AFSYYGP++ VW+ARNPPGF FVEFED RDAEDAVRG DG+ I G RVRV
Sbjct: 10 TGAGKGELERAFSYYGPLRTVWIARNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRV 69
Query: 108 EMS 110
E+S
Sbjct: 70 ELS 72
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 93.6 bits (231), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 43/66 (65%), Positives = 52/66 (78%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+ K ++E AF YYGP+++VWVARNPPGF FVEFED RDA DAVR DGR + G RVRVE
Sbjct: 84 NGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRDLDGRTLCGCRVRVE 143
Query: 109 MSNPQK 114
+SN +K
Sbjct: 144 LSNGEK 149
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 93.2 bits (230), Expect = 2e-19, Method: Compositional matrix adjust.
Identities = 43/66 (65%), Positives = 52/66 (78%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
+ K ++E AF YYGP+++VWVARNPPGF FVEFED RDA DAVR DGR + G RVRVE
Sbjct: 84 NGNKTELERAFGYYGPLRSVWVARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVE 143
Query: 109 MSNPQK 114
+SN +K
Sbjct: 144 LSNGEK 149
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 32/59 (54%), Positives = 40/59 (67%), Gaps = 2/59 (3%)
Query: 53 EDIEDAFSYYGPIKNVWVA--RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
+DIED F YG I+++ + R P F FVEFED RDAEDAV G DG + +G R+RVE
Sbjct: 37 KDIEDVFYKYGAIRDIDLKNRRGGPPFAFVEFEDPRDAEDAVYGRDGYDYDGYRLRVEF 95
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 45/80 (56%), Gaps = 7/80 (8%)
Query: 36 MLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAED 90
M+ + V + TS + + F YG + +V++ R P GF FV F DRRDA+D
Sbjct: 13 MITLKVDNLTYRTS--PDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQD 70
Query: 91 AVRGFDGREINGRRVRVEMS 110
A DG E++GR +RV+++
Sbjct: 71 AEAAMDGAELDGRELRVQVA 90
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 53.5 bits (127), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 41 VSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGF 95
+ + S +T+ D+ + FS YGPI +V + +R GF FV FE+ DA++A
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 96 DGREINGRRVRVEMS 110
+G E++GRR+RV+ S
Sbjct: 109 NGMELDGRRIRVDFS 123
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 41 VSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGF 95
+ + S +T+ D+ + FS YGPI +V + +R GF FV FE+ DA++A
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 96 DGREINGRRVRVEMS 110
+G E++GRR+RV+ S
Sbjct: 75 NGMELDGRRIRVDFS 89
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 52.8 bits (125), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 45/75 (60%), Gaps = 5/75 (6%)
Query: 41 VSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGF 95
+ + S +T+ D+ + FS YGPI +V + +R GF FV FE+ DA++A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96 DGREINGRRVRVEMS 110
+G E++GRR+RV+ S
Sbjct: 78 NGMELDGRRIRVDFS 92
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 52.0 bits (123), Expect = 4e-07, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 42/69 (60%), Gaps = 5/69 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S + ++ +E FS YG I V V ++ GFGFV FE+ DA+DA+ +G+ ++
Sbjct: 21 SFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVD 80
Query: 102 GRRVRVEMS 110
GR++RV+ +
Sbjct: 81 GRQIRVDQA 89
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 51.2 bits (121), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 24/57 (42%), Positives = 36/57 (63%), Gaps = 5/57 (8%)
Query: 59 FSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
F YG + +V++ R+ GF FV F D+RDAEDA+ DG ++GR +RV+M+
Sbjct: 91 FEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQMA 147
>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 = 50.8 bits (120), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 40/66 (60%), Gaps = 5/66 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
++ + + F YG + +V++ R+ GF FV F D+RDAEDA+ DG ++GR
Sbjct: 59 TSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDGAVLDGRE 118
Query: 105 VRVEMS 110
+RV+M+
Sbjct: 119 LRVQMA 124
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.1 bits (118), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 5/72 (6%)
Query: 41 VSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGF 95
+ + S +T+ D+ + FS YGPI +V + +R GF FV FE+ DA++A
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 96 DGREINGRRVRV 107
+G E++GRR+RV
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 49.3 bits (116), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 41/71 (57%), Gaps = 6/71 (8%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGR 103
S+T E +++ FS +G + NV + + P GFGFVE ++ +E A+ D + GR
Sbjct: 12 SATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSE-AIAKLDNTDFMGR 70
Query: 104 RVRVEMSNPQK 114
+RV +NP+K
Sbjct: 71 TIRVTEANPKK 81
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 48.9 bits (115), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 24/70 (34%), Positives = 43/70 (61%), Gaps = 5/70 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T+E ++D FS GP+ + + + P G+GF E++D+ A A+R +GRE +GR
Sbjct: 20 ATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSGRA 79
Query: 105 VRVEMSNPQK 114
+RV+ + +K
Sbjct: 80 LRVDNAASEK 89
>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 = 48.5 bits (114), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 7/77 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAV 92
++V+ V T+ +K + F YGPIK + + + P G+ F+E+E RD A
Sbjct: 104 TLFVARVNYDTTESK--LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 93 RGFDGREINGRRVRVEM 109
+ DG++I+GRRV V++
Sbjct: 162 KHADGKKIDGRRVLVDV 178
>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 = 47.8 bits (112), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 44/77 (57%), Gaps = 7/77 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAV 92
++V+ V T+ +K + F YGPIK + + + P G+ F+E+E RD A
Sbjct: 104 TLFVARVNYDTTESK--LRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAY 161
Query: 93 RGFDGREINGRRVRVEM 109
+ DG++I+GRRV V++
Sbjct: 162 KHADGKKIDGRRVLVDV 178
>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 = 46.6 bits (109), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 21 QEAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP----- 75
Q I D + AR IYV+ V S +DI+ F +G IK+ +AR+P
Sbjct: 110 QAQPIIDQLAEEARAFNRIYVASVHQDLSD--DDIKSVFEAFGKIKSATLARDPTTGKHK 167
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GF+E+E + ++DAV + ++ G+ +RV
Sbjct: 168 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Score = 35.4 bits (80), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 52 KEDIEDAFSYYGPIKNV---W--VARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
++ I AF+ +GPIK++ W V GF FVE+E A+ A+ + + GR ++
Sbjct: 42 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 101
Query: 107 V 107
V
Sbjct: 102 V 102
>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 = 45.4 bits (106), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 21 QEAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP----- 75
Q I D + AR IYV+ V S +DI+ F +G IK+ +AR+P
Sbjct: 95 QAQPIIDQLAEEARAFNRIYVASVHQDLSD--DDIKSVFEAFGKIKSCTLARDPTTGKHK 152
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GF+E+E + ++DAV + ++ G+ +RV
Sbjct: 153 GYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Score = 35.8 bits (81), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 52 KEDIEDAFSYYGPIKNV---W--VARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
++ I AF+ +GPIK++ W V GF FVE+E A+ A+ + + GR ++
Sbjct: 27 EDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIK 86
Query: 107 V 107
V
Sbjct: 87 V 87
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 45.1 bits (105), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 49/92 (53%), Gaps = 7/92 (7%)
Query: 21 QEAEIEDPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP----- 75
Q I D + AR IYV+ V S +DI+ F +G IK+ +AR+P
Sbjct: 94 QAQPIIDQLAEEARAFNRIYVASVHQDLSD--DDIKSVFEAFGKIKSCTLARDPTTGKHK 151
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GF+E+E + ++DAV + ++ G+ +RV
Sbjct: 152 GYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Score = 34.7 bits (78), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 5/61 (8%)
Query: 52 KEDIEDAFSYYGPIKNV---W--VARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
++ I AF+ +GPIK++ W V GF FVE+E A+ A+ + + GR ++
Sbjct: 26 EDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGGRNIK 85
Query: 107 V 107
V
Sbjct: 86 V 86
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 5/64 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T+EDI D F+ YG IKN+ + + G+ VE+E ++A+ A+ G +G+++ G+
Sbjct: 19 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 78
Query: 105 VRVE 108
+ V+
Sbjct: 79 ISVD 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 44.3 bits (103), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 5/63 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T EDI+ AF+ +G I + V ++ G+GFV F ++ DAE+A+ G+ + GR++
Sbjct: 28 TTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
Query: 106 RVE 108
R
Sbjct: 88 RTN 90
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 5/64 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T+EDI D F+ YG IKN+ + + G+ VE+E ++A+ A+ G +G+++ G+
Sbjct: 19 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 78
Query: 105 VRVE 108
+ V+
Sbjct: 79 ISVD 82
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 39/65 (60%), Gaps = 5/65 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T EDI+ AF+ +G I + V ++ G+GFV F ++ DAE+A++ G+ + GR++
Sbjct: 28 TTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
Query: 106 RVEMS 110
R +
Sbjct: 88 RTNWA 92
>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 = 43.9 bits (102), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 46/76 (60%), Gaps = 7/76 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAV 92
+++V+ V +T+EDI D F+ YG IKN+ + + G+ VE+E ++A+ A+
Sbjct: 24 ILFVTGV--HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 81
Query: 93 RGFDGREINGRRVRVE 108
G +G+++ G+ + V+
Sbjct: 82 EGLNGQDLMGQPISVD 97
>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 = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 5/64 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T+EDI D F+ YG IKN+ + + G+ VE+E ++A+ A+ G +G+++ G+
Sbjct: 19 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 78
Query: 105 VRVE 108
+ V+
Sbjct: 79 ISVD 82
>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 = 43.5 bits (101), Expect = 1e-04, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 40/64 (62%), Gaps = 5/64 (7%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T+EDI D F+ YG IKN+ + + G+ VE+E ++A+ A+ G +G+++ G+
Sbjct: 21 ATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLNGQDLMGQP 80
Query: 105 VRVE 108
+ V+
Sbjct: 81 ISVD 84
>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 = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 46/76 (60%), Gaps = 7/76 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAV 92
+++V+ V +T+EDI D F+ YG IKN+ + + G+ VE+E ++A+ A+
Sbjct: 25 ILFVTGV--HEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAM 82
Query: 93 RGFDGREINGRRVRVE 108
G +G+++ G+ + V+
Sbjct: 83 EGLNGQDLMGQPISVD 98
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 43.5 bits (101), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 10/84 (11%)
Query: 32 IARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRR 86
+ R ++V Y+ T+ + + F YGPI++V + R G+GFV+F+
Sbjct: 41 VLRNLMVNYIP-----TTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGS 95
Query: 87 DAEDAVRGFDGREINGRRVRVEMS 110
A+ A+ G +G I +R++V ++
Sbjct: 96 SAQQAIAGLNGFNILNKRLKVALA 119
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 46/89 (51%), Gaps = 8/89 (8%)
Query: 27 DPVMMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRR 86
DP M +R + ++V+ K D+E FS YG I V + GF FV++ + R
Sbjct: 10 DPRSMNSRVFIGNLNTLVV-----KKSDVEAIFSKYGKIVGCSVHK---GFAFVQYVNER 61
Query: 87 DAEDAVRGFDGREINGRRVRVEMSNPQKM 115
+A AV G DGR I G+ + + ++ K+
Sbjct: 62 NARAAVAGEDGRMIAGQVLDINLAAEPKV 90
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 42.7 bits (99), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 36/67 (53%), Gaps = 3/67 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S + T +++ F YGP+ + ++ + FV E DA +A+RG D E G+R+
Sbjct: 19 SPTCTNQELRAKFEEYGPVIECDIVKD---YAFVHMERAEDAVEAIRGLDNTEFQGKRMH 75
Query: 107 VEMSNPQ 113
V++S +
Sbjct: 76 VQLSTSR 82
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 42.4 bits (98), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 40/71 (56%), Gaps = 7/71 (9%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREING 102
S S+T+E +++ F IK V +N G+ F+EF DA++A+ + REI G
Sbjct: 24 SYSATEETLQEVFEKATFIK---VPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEG 80
Query: 103 RRVRVEMSNPQ 113
R +R+E+ P+
Sbjct: 81 RAIRLELQGPR 91
>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 = 42.0 bits (97), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/67 (32%), Positives = 36/67 (53%), Gaps = 4/67 (5%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
S TKE++E+ +G +K++ + N P G +VE+E+ A AV DG I
Sbjct: 28 SCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKENI 87
Query: 105 VRVEMSN 111
++V +SN
Sbjct: 88 IKVAISN 94
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 41.6 bits (96), Expect = 5e-04, Method: Composition-based stats.
Identities = 24/61 (39%), Positives = 38/61 (62%), Gaps = 6/61 (9%)
Query: 51 TKEDIEDAFSYYGPIK--NVWVARNPP----GFGFVEFEDRRDAEDAVRGFDGREINGRR 104
TK+ I + FS YG IK ++ V R P G+ +VEFE+ +AE A++ DG +I+G+
Sbjct: 17 TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDGQE 76
Query: 105 V 105
+
Sbjct: 77 I 77
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 41.6 bits (96), Expect = 6e-04, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 5/73 (6%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVW-----VARNPPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S +S++ED+E FS YGP+ + + + P GF FV F A A DG+
Sbjct: 17 SYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVDGQVFQ 76
Query: 102 GRRVRVEMSNPQK 114
GR + V S +K
Sbjct: 77 GRMLHVLPSTIKK 89
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 40.8 bits (94), Expect = 9e-04, Method: Composition-based stats.
Identities = 23/66 (34%), Positives = 37/66 (56%), Gaps = 4/66 (6%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVA----RNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
S +T+E I + FS G IK + + + GF FVE+ R DAE+A+R +G ++
Sbjct: 27 SFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYINGTRLDD 86
Query: 103 RRVRVE 108
R +R +
Sbjct: 87 RIIRTD 92
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
+T+++I F YG + + +N +GFV ED+ AEDA+R +++G + VE
Sbjct: 20 ATEQEIRSLFEQYGKVLECDIIKN---YGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEA 76
Query: 110 S 110
S
Sbjct: 77 S 77
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 8/70 (11%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP--------GFGFVEFEDRRDAEDAVRGFDGREI 100
S+T+E ++ FS G IK+ +++ GFGFVE++ A+ A++ G +
Sbjct: 16 STTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQKALKQLQGHTV 75
Query: 101 NGRRVRVEMS 110
+G ++ V +S
Sbjct: 76 DGHKLEVRIS 85
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 40.4 bits (93), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 55 IEDAFSYYGPIKNVWVARN----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
++ F +GPI V + ++ GF F+ FE+ DA++A + +G+ ++G+ ++VE +
Sbjct: 24 LKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQA 83
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 39.7 bits (91), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 3/59 (5%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
K D+E FS YG + V + G+ FV++ + R A AV G +GR + G+ + + M+
Sbjct: 42 KSDVETIFSKYGRVAGCSVHK---GYAFVQYSNERHARAAVLGENGRVLAGQTLDINMA 97
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 38.9 bits (89), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDG 97
T++D+ED FS +G I N V + G F+ F+ R +AE+A+ F+G
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 35.4 bits (80), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++ FS G +++ + R+ G+GFV + +DAE A+ +G + + +
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 106 RVEMSNP 112
+V + P
Sbjct: 75 KVSYARP 81
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/52 (36%), Positives = 30/52 (57%), Gaps = 5/52 (9%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDG 97
T++D+ED FS +G I N V + G F+ F+ R +AE+A+ F+G
Sbjct: 101 TQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSFNG 152
Score = 35.4 bits (80), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++ FS G +++ + R+ G+GFV + +DAE A+ +G + + +
Sbjct: 15 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 74
Query: 106 RVEMSNP 112
+V + P
Sbjct: 75 KVSYARP 81
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 38.9 bits (89), Expect = 0.004, Method: Composition-based stats.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 54 DIEDAFSYYGPIKNVWV---ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
D+ F +G I +V + R GFGFV FE+ DA+ A G + GR++ V +
Sbjct: 31 DLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 90
Query: 111 NPQKM 115
+ M
Sbjct: 91 TARVM 95
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.9 bits (89), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 48 TSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T T+ED + F YG V++ R+ GFGF+ E R AE A DG + R +R+
Sbjct: 32 TDITEEDFKRLFERYGEPSEVFINRDR-GFGFIRLESRTLAEIAKAELDGTILKSRPLRI 90
Query: 108 EMSN 111
+
Sbjct: 91 RFAT 94
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 38.5 bits (88), Expect = 0.004, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 37/73 (50%), Gaps = 10/73 (13%)
Query: 53 EDIED-----AFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
E+++D AF +G I ++ + GF FVEFE DA A+ + E+ G
Sbjct: 22 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 81
Query: 103 RRVRVEMSNPQKM 115
R +RV ++ P ++
Sbjct: 82 RTIRVNLAKPMRI 94
>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 = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVA-----RNPPGFGFVEFEDRRDAEDAV 92
+YV + S +T+E I + FS G IK + + + GF FVE+ R DAE+A+
Sbjct: 41 TLYVGNL--SFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 93 RGFDGREINGRRVRVE 108
R +G ++ R +R +
Sbjct: 99 RYINGTRLDDRIIRTD 114
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 22/66 (33%), Positives = 34/66 (51%), Gaps = 2/66 (3%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP--GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
T E++ D F YGPI+ + V P G +V +ED DA++AV G ++ R + V
Sbjct: 21 TAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHLSGFNVSNRYLVVL 80
Query: 109 MSNPQK 114
N +
Sbjct: 81 YYNANR 86
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 37.7 bits (86), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/65 (32%), Positives = 32/65 (49%), Gaps = 3/65 (4%)
Query: 54 DIEDAFSYYGPIKNVWVA---RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
D+ F +G I +V + R GFGFV FE+ DA+ A G + GR++ V +
Sbjct: 45 DLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNA 104
Query: 111 NPQKM 115
+ M
Sbjct: 105 TARVM 109
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 37.4 bits (85), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 18/57 (31%), Positives = 34/57 (59%), Gaps = 5/57 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREING 102
T++++E FS YG I + + G GF+ F+ R +AE+A++G +G++ +G
Sbjct: 101 TQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGLNGQKPSG 157
Score = 36.6 bits (83), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E+ F G I++ + R+ G+GFV + D +DAE A+ +G + + +
Sbjct: 15 TQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLNGLRLQTKTI 74
Query: 106 RVEMSNP 112
+V + P
Sbjct: 75 KVSYARP 81
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 18/64 (28%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
S + T +++ F G + V ++ + FV E DA+ A+ +G+E+ G+R+
Sbjct: 18 SAACTSQELRSLFERRGRVIECDVVKD---YAFVHMEKEADAKAAIAQLNGKEVKGKRIN 74
Query: 107 VEMS 110
VE+S
Sbjct: 75 VELS 78
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 37.0 bits (84), Expect = 0.015, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E I D S GP+ N+ + +P G+ F+EF D + AVR +G ++ R +
Sbjct: 15 TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 74
Query: 106 RVEMSN 111
+ S+
Sbjct: 75 KCGYSS 80
>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 = 36.6 bits (83), Expect = 0.016, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E I D S GP+ N+ + +P G+ F+EF D + AVR +G ++ R +
Sbjct: 16 TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 75
Query: 106 RVEMSN 111
+ S+
Sbjct: 76 KCGYSS 81
>pdb|1O0P|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
Length = 104
Score = 36.6 bits (83), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 53 EDIEDAFSYYGPIKNVWVAR-----NPPGFG--FVEFEDRRDAEDAVRGFDGREINGRRV 105
ED+ D S YG +K++ + R PG G FVEF D + A++G GR+ R V
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 106 RVEMSNP 112
+ +P
Sbjct: 89 VTKYCDP 95
>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 = 36.6 bits (83), Expect = 0.017, Method: Composition-based stats.
Identities = 13/32 (40%), Positives = 23/32 (71%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
G+GFV F + DA++A+ G+++NGR +R+
Sbjct: 44 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 75
>pdb|1OPI|A Chain A, Solution Structure Of The Third Rna Recognition Motif
(Rrm) Of U2af65 In Complex With An N-Terminal Sf1
Peptide
pdb|2M0G|B Chain B, Structure, Phosphorylation And U2af65 Binding Of The
Nterminal Domain Of Splicing Factor 1 During 3 Splice
Site Recognition
Length = 104
Score = 36.6 bits (83), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 34/67 (50%), Gaps = 7/67 (10%)
Query: 53 EDIEDAFSYYGPIKNVWVAR-----NPPGFG--FVEFEDRRDAEDAVRGFDGREINGRRV 105
ED+ D S YG +K++ + R PG G FVEF D + A++G GR+ R V
Sbjct: 29 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAMQGLTGRKFANRVV 88
Query: 106 RVEMSNP 112
+ +P
Sbjct: 89 VTKYCDP 95
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 5/71 (7%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREIN 101
S + + D+++ F +G I +++A++ GF F+ F R DA A+ G G +
Sbjct: 24 SEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGVSGFGYD 83
Query: 102 GRRVRVEMSNP 112
+ VE + P
Sbjct: 84 HLILNVEWAKP 94
>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 = 36.6 bits (83), Expect = 0.020, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 5/66 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+E I D S GP+ N+ + +P G+ F+EF D + AVR +G ++ R +
Sbjct: 17 TEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQLGSRFL 76
Query: 106 RVEMSN 111
+ S+
Sbjct: 77 KCGYSS 82
>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 = 36.2 bits (82), Expect = 0.021, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
T+E++ F YG V++ ++ GFGF+ E R AE A D + G+++RV +
Sbjct: 28 TEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 86
>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 = 0.022, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 37/66 (56%), Gaps = 7/66 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVR 93
+YVS L T S KE +E FS YG I + + G GF+ F+ R +AE+A++
Sbjct: 93 LYVS-GLPKTMSQKE-MEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 94 GFDGRE 99
G +G++
Sbjct: 151 GLNGQK 156
Score = 35.0 bits (79), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+++ + F G I++ + R+ G+GFV + D DA+ A+ +G ++ + +
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 106 RVEMSNP 112
+V + P
Sbjct: 77 KVSYARP 83
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.2 bits (82), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
T+E++ F YG V++ ++ GFGF+ E R AE A D + G+++RV +
Sbjct: 35 TEEEMRKLFEKYGKAGEVFIHKDK-GFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFA 93
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 36.2 bits (82), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 13/33 (39%), Positives = 23/33 (69%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
G+GFV F + DA++A+ G+++NGR +R+
Sbjct: 130 GYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRIN 162
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 35.8 bits (81), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 29/58 (50%), Gaps = 5/58 (8%)
Query: 58 AFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
AF +G I ++ + GF FVEFE DA A+ + E+ GR +RV ++
Sbjct: 83 AFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLA 140
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 35.8 bits (81), Expect = 0.031, Method: Composition-based stats.
Identities = 16/66 (24%), Positives = 36/66 (54%), Gaps = 3/66 (4%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
+ + T+E +E AFS +G ++ V + + F+ F++R A A+ +G+++ G +
Sbjct: 20 ANTVTEEILEKAFSQFGKLERV---KKLKDYAFIHFDERDGAVKAMEEMNGKDLEGENIE 76
Query: 107 VEMSNP 112
+ + P
Sbjct: 77 IVFAKP 82
>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 = 0.032, Method: Composition-based stats.
Identities = 26/69 (37%), Positives = 39/69 (56%), Gaps = 13/69 (18%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPI--------KNVWVARNPPGFGFVEFEDRRDAED 90
+YVS L T S KE +E FS YG I + V+R G GF+ F+ R +AE+
Sbjct: 4 LYVS-GLPKTMSQKE-MEQLFSQYGRIITSRILLDQATGVSR---GVGFIRFDKRIEAEE 58
Query: 91 AVRGFDGRE 99
A++G +G++
Sbjct: 59 AIKGLNGQK 67
>pdb|4FXW|A Chain A, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
pdb|4FXW|C Chain C, Structure Of Phosphorylated Sf1 Complex With U2af65-uhm
Domain
Length = 106
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 53 EDIEDAFSYYGPIKNVWVAR-----NPPGFG--FVEFEDRRDAEDAVRGFDGREINGRRV 105
ED+ D S YG +K++ + R PG G FVEF D + A +G GR+ R V
Sbjct: 31 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 90
Query: 106 RVEMSNP 112
+ +P
Sbjct: 91 VTKYCDP 97
>pdb|3V4M|A Chain A, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
pdb|3V4M|B Chain B, Crystal Structure Of A Rna Binding Domain Of A U2 Small
Nuclear Ribonucleoprotein Auxiliary Factor 2 (U2af) From
Mus Musculus At 1.80 A Resolution
Length = 105
Score = 35.4 bits (80), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 33/67 (49%), Gaps = 7/67 (10%)
Query: 53 EDIEDAFSYYGPIKNVWVAR-----NPPGFG--FVEFEDRRDAEDAVRGFDGREINGRRV 105
ED+ D S YG +K++ + R PG G FVEF D + A +G GR+ R V
Sbjct: 30 EDVRDECSKYGLVKSIEIPRPVDGVEVPGCGKIFVEFTSVFDCQKAXQGLTGRKFANRVV 89
Query: 106 RVEMSNP 112
+ +P
Sbjct: 90 VTKYCDP 96
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 35.4 bits (80), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAV 92
+++V+ + + +++I++ F YG IKN+ + + G+ VE+E + A A
Sbjct: 28 ILFVTSI--HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 85
Query: 93 RGFDGREINGRRVRVE 108
+G EI G+ ++V+
Sbjct: 86 EALNGAEIMGQTIQVD 101
>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 = 0.044, Method: Composition-based stats.
Identities = 16/69 (23%), Positives = 36/69 (52%), Gaps = 5/69 (7%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGR 103
+ T++++ FS G +++ + R+ G+GFV + +DAE A+ +G + +
Sbjct: 30 NXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSK 89
Query: 104 RVRVEMSNP 112
++V + P
Sbjct: 90 TIKVSYARP 98
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.047, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP--GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
T E++ D F YGPI+ + V P G +V +ED DA++A G + R + V
Sbjct: 25 TAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL 84
Query: 109 MSN 111
N
Sbjct: 85 YYN 87
>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 = 35.0 bits (79), Expect = 0.049, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++++ FS G +++ + R+ G+GFV + +DAE A+ +G + + +
Sbjct: 17 TQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLNGLRLQSKTI 76
Query: 106 RVEMSNP 112
+V + P
Sbjct: 77 KVSYARP 83
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 35.0 bits (79), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP--GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
T E++ D F YGPI+ + V P G +V +ED DA++A G + R + V
Sbjct: 31 TAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL 90
Query: 109 MSNPQK 114
N +
Sbjct: 91 YYNANR 96
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 35.0 bits (79), Expect = 0.060, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 53 EDIED-----AFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
E+++D AF +G I ++ + GF FVEFE DA A+ + E+ G
Sbjct: 15 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 74
Query: 103 RRVRVEMS 110
R +RV ++
Sbjct: 75 RTIRVNLA 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 = 35.0 bits (79), Expect = 0.060, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 53 EDIED-----AFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
E+++D AF +G I ++ + GF FVEFE DA A+ + E+ G
Sbjct: 12 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 71
Query: 103 RRVRVEMS 110
R +RV ++
Sbjct: 72 RTIRVNLA 79
>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 = 35.0 bits (79), Expect = 0.060, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 34/68 (50%), Gaps = 10/68 (14%)
Query: 53 EDIED-----AFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREING 102
E+++D AF +G I ++ + GF FVEFE DA A+ + E+ G
Sbjct: 17 EEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNESELFG 76
Query: 103 RRVRVEMS 110
R +RV ++
Sbjct: 77 RTIRVNLA 84
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 35.0 bits (79), Expect = 0.060, Method: Composition-based stats.
Identities = 16/67 (23%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+++ + F G I++ + R+ G+GFV + D DA+ A+ +G ++ + +
Sbjct: 17 TQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLNGLKLQTKTI 76
Query: 106 RVEMSNP 112
+V + P
Sbjct: 77 KVSYARP 83
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 35.0 bits (79), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPP--GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
T E++ D F YGPI+ + V P G +V +ED DA++A G + R + V
Sbjct: 31 TAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNACDHLSGFNVCNRYLVVL 90
Query: 109 MSNPQK 114
N +
Sbjct: 91 YYNANR 96
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 34.7 bits (78), Expect = 0.063, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 3/54 (5%)
Query: 57 DAFSYYGPI---KNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
D FS +G I K V G+GFV FE + AE A+ +G +N R+V V
Sbjct: 30 DTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 83
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 34.7 bits (78), Expect = 0.071, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 38/71 (53%), Gaps = 6/71 (8%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVAR----NPPGFGFVEFEDRRDAEDAVRGFDGREING 102
S +T+E ++++F G ++ V + GFGFV+F DA+ A + EI+G
Sbjct: 24 SEDTTEETLKESFD--GSVRARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAMEDGEIDG 81
Query: 103 RRVRVEMSNPQ 113
+V ++ + P+
Sbjct: 82 NKVTLDWAKPK 92
>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 = 34.3 bits (77), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 55 IEDAFSYYGPIKNVWVA---RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ D FS +G I + V G+GFV FE + AE A+ +G +N R+V V
Sbjct: 115 LYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 170
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 51 TKEDIEDAFSYYGPIKNV-----WVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ + + FS GPI ++ + R G+ +V F+ DAE A+ + I G+ V
Sbjct: 23 TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 82
Query: 106 RVEMS 110
R+ S
Sbjct: 83 RIMWS 87
>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 = 34.3 bits (77), Expect = 0.093, Method: Composition-based stats.
Identities = 13/31 (41%), Positives = 23/31 (74%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVR 106
G+GFV F ++ DAE+A++ G+ + GR++R
Sbjct: 49 GYGFVSFFNKWDAENAIQQMGGQWLGGRQIR 79
>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 = 34.3 bits (77), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 50 STKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
ST +D+E FS G I + + + +P G+ ++EF + R++ DA D GR
Sbjct: 48 STAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAE-RNSVDAAVAMDETVFRGRT 106
Query: 105 VRV 107
++V
Sbjct: 107 IKV 109
>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 = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 55 IEDAFSYYGPIKNVWVA---RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ D FS +G I + V G+GFV FE + AE A+ +G +N R+V V
Sbjct: 22 LYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 77
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 7/71 (9%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPPG------FGFVEFEDRRDAEDAVRGF-DGREING 102
+ + +I + FS +G +K V + + G FGFV+F ++DA+ A + G
Sbjct: 27 ANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNALCHSTHLYG 86
Query: 103 RRVRVEMSNPQ 113
RR+ +E ++ +
Sbjct: 87 RRLVLEWADSE 97
>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 = 33.9 bits (76), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 41/76 (53%), Gaps = 7/76 (9%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAV 92
+++V+ + + +++I++ F YG IKN+ + + G+ VE+E + A A
Sbjct: 74 ILFVTSI--HEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAK 131
Query: 93 RGFDGREINGRRVRVE 108
+G EI G+ ++V+
Sbjct: 132 EALNGAEIMGQTIQVD 147
>pdb|2XNQ|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.9 bits (76), Expect = 0.12, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN-GRRVRVEM 109
+KED+ FS YG I + + FGF++F++ + DA+ + +E+N G+++ +E+
Sbjct: 36 SKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAIE-XESQEMNFGKKLILEV 91
Query: 110 SN 111
S+
Sbjct: 92 SS 93
>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 = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 55 IEDAFSYYGPIKNVWVA---RNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ D FS +G I + V G+GFV FE + AE A+ +G +N R+V V
Sbjct: 120 LYDTFSAFGNILSCKVVCDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFV 175
Score = 29.3 bits (64), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 51 TKEDIEDAFSYYGPIKNV-----WVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T+ + + FS GPI ++ + R G+ +V F+ DAE A+ + I G+ V
Sbjct: 28 TEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
Query: 106 RVEMS 110
R+ S
Sbjct: 88 RIMWS 92
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 33.9 bits (76), Expect = 0.13, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 32/62 (51%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++ + F +G I N+ + ++ G+GF+ F D A A+ +G E+ GR +
Sbjct: 18 TEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQLNGFELAGRPM 77
Query: 106 RV 107
RV
Sbjct: 78 RV 79
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 34/68 (50%), Gaps = 4/68 (5%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
C+ T E+++ F YG + +V++ + F FV F D + A+ G ++ + +
Sbjct: 19 CTEDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLC----GEDLIIKGI 74
Query: 106 RVEMSNPQ 113
V +SN +
Sbjct: 75 SVHISNAE 82
>pdb|2L41|A Chain A, Nab3 Rrm - Ucuu Complex
Length = 77
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN-GRRVRVEM 109
+KED+ FS YG I + + FGF++F++ + DA+ + +E+N G+++ +E+
Sbjct: 16 SKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAIE-CESQEMNFGKKLILEV 71
Query: 110 SN 111
S+
Sbjct: 72 SS 73
>pdb|2XNR|A Chain A, Structural Insights Into Cis Element Recognition Of Non-
Polyadenylated Rnas By The Nab3-Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.21, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN-GRRVRVEM 109
+KED+ FS YG I + + FGF++F++ + DA+ + +E+N G+++ +E+
Sbjct: 36 SKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAIE-CESQEMNFGKKLILEV 91
Query: 110 SN 111
S+
Sbjct: 92 SS 93
>pdb|2KVI|A Chain A, Structure Of Nab3 Rrm
Length = 96
Score = 32.7 bits (73), Expect = 0.29, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 38/62 (61%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREIN-GRRVRVEM 109
+KED+ FS YG I + + FGF++F++ + DA+ + +E+N G+++ +E+
Sbjct: 24 SKEDLFRIFSPYGHIMQINIKN---AFGFIQFDNPQSVRDAIE-CESQEMNFGKKLILEV 79
Query: 110 SN 111
S+
Sbjct: 80 SS 81
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 32.3 bits (72), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/68 (25%), Positives = 36/68 (52%), Gaps = 4/68 (5%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
C+ T++++ + FS YG + +V++ + F FV F D + A+ G ++ + +
Sbjct: 13 CTGDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLC----GEDLIIKGI 68
Query: 106 RVEMSNPQ 113
V +SN +
Sbjct: 69 SVHISNAE 76
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 6/74 (8%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRGFDGREI 100
S +T+E + + F +G +K V R+P GFGFV F D+ D V E+
Sbjct: 33 LSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGV-DKVLAQSRHEL 91
Query: 101 NGRRVRVEMSNPQK 114
+ + + +++ P++
Sbjct: 92 DSKTIDPKVAFPRR 105
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 32.3 bits (72), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 27/54 (50%), Gaps = 3/54 (5%)
Query: 54 DIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
++ + F +GP+K V + GF FVEFE+ A A+ G+ + + V
Sbjct: 47 ELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGKSFANQPLEV 97
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 32.3 bits (72), Expect = 0.36, Method: Composition-based stats.
Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 3/59 (5%)
Query: 52 KEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMS 110
+ ++ + F +GP+K V + GF FVEFE+ A A+ G+ + + V S
Sbjct: 18 ESELNEIFGPFGPMKEVKILN---GFAFVEFEEAESAAKAIEEVHGKSFANQPLEVVYS 73
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain
Of Mouse Musashi1
Length = 77
Score = 32.0 bits (71), Expect = 0.40, Method: Composition-based stats.
Identities = 16/44 (36%), Positives = 24/44 (54%), Gaps = 5/44 (11%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDR 85
S +T+E + + F +G +K V R+P GFGFV F D+
Sbjct: 9 SWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 52
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 32.0 bits (71), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 6/65 (9%)
Query: 54 DIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVE 108
++ + F +G + V + + P GFGF+ FED + + AV +I G++V V+
Sbjct: 26 ELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVN-MHFHDIMGKKVEVK 84
Query: 109 MSNPQ 113
+ P+
Sbjct: 85 RAEPR 89
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 31.6 bits (70), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 1/61 (1%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWV-ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ +ED+ S +G I+ + + R+P G V F D +A+ ++ DGR GR++
Sbjct: 37 NEIREDLRVECSKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Query: 108 E 108
+
Sbjct: 97 Q 97
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 31.6 bits (70), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/56 (30%), Positives = 30/56 (53%), Gaps = 5/56 (8%)
Query: 57 DAFSYYGPIKNVWVARN-----PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
+ F GP+ N + ++ G+GFVEF DA+ A++ D ++ G+ +RV
Sbjct: 34 ELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRV 89
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 31.6 bits (70), Expect = 0.64, Method: Composition-based stats.
Identities = 17/52 (32%), Positives = 30/52 (57%), Gaps = 3/52 (5%)
Query: 47 STSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGR 98
+T+ T+E +E +FS +G ++ V + + FV FEDR A A+ +G+
Sbjct: 24 ATTVTEEILEKSFSEFGKLERV---KKLKDYAFVHFEDRGAAVKAMDEMNGK 72
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 31.2 bits (69), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 42/86 (48%), Gaps = 15/86 (17%)
Query: 38 VIYVSIVLCSTSSTKEDIEDAFSYYG----------PIKNVWVAR---NPPGFGFVEFED 84
IYV + + S T +D+ D F G P+ ++++ + P G V +ED
Sbjct: 17 AIYVQGL--NDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYED 74
Query: 85 RRDAEDAVRGFDGREINGRRVRVEMS 110
A+ AV FDG++ G +++V ++
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKVSLA 100
>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 = 30.8 bits (68), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 35/63 (55%), Gaps = 8/63 (12%)
Query: 50 STKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFEDRRDAEDAVRG---FDGREIN 101
+T++++ + F YG + ++ + ++P GFGF+ FE ++ V+ DG+ I+
Sbjct: 15 TTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVKTQHILDGKVID 74
Query: 102 GRR 104
+R
Sbjct: 75 PKR 77
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 54 DIEDAFSYYGPIKNVWVARNPPGFGF----VEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
DI++ F+ +G +K V + G V FE R DA A++ + G ++GR + +++
Sbjct: 51 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 110
Query: 110 SNPQ 113
Q
Sbjct: 111 VASQ 114
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 33/60 (55%), Gaps = 4/60 (6%)
Query: 54 DIEDAFSYYGPIKNVWVARNPPGFGF----VEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
DI++ F+ +G +K V + G V FE + DA A++ ++G ++GR + +++
Sbjct: 44 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQL 103
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 4/64 (6%)
Query: 54 DIEDAFSYYGPIKNVWVARNPPGFGF----VEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
DI++ F+ +G +K V + G V FE R DA A++ + G ++GR + +++
Sbjct: 51 DIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQL 110
Query: 110 SNPQ 113
Q
Sbjct: 111 VASQ 114
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.0 bits (66), Expect = 1.5, Method: Composition-based stats.
Identities = 26/87 (29%), Positives = 39/87 (44%), Gaps = 9/87 (10%)
Query: 25 IEDPV----MMIARYMLVIYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFV 80
+EDP + AR +L +S + + KE EDA I+ V G ++
Sbjct: 4 LEDPCTSKKVRAARTLLAKNLSFNI-TEDELKEVFEDALE----IRLVSQDGKSKGIAYI 58
Query: 81 EFEDRRDAEDAVRGFDGREINGRRVRV 107
EF+ DAE + G EI+GR V +
Sbjct: 59 EFKSEADAEKNLEEKQGAEIDGRSVSL 85
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 33/62 (53%), Gaps = 5/62 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP-----PGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
T++ + F +G I+++ + + G+GF+ F D A+ A+ +G E+ GR +
Sbjct: 39 TEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAGRPM 98
Query: 106 RV 107
+V
Sbjct: 99 KV 100
>pdb|3NYB|B Chain B, Structure And Function Of The Polymerase Core Of Tramp, A
Rna Surveillance Complex
Length = 83
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 146 CYECGGRGHYARDC 159
CY CGG+GH+ DC
Sbjct: 49 CYNCGGKGHFGDDC 62
Score = 30.0 bits (66), Expect = 1.7, Method: Composition-based stats.
Identities = 9/14 (64%), Positives = 11/14 (78%)
Query: 221 CYECGGRGHYARDC 234
CY CGG+GH+ DC
Sbjct: 49 CYNCGGKGHFGDDC 62
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 30.0 bits (66), Expect = 1.9, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 32/73 (43%), Gaps = 13/73 (17%)
Query: 51 TKEDIEDAFSYYG----------PIKNVWVARNP---PGFGFVEFEDRRDAEDAVRGFDG 97
T E + D F G P+ N++ R G V F+D A+ A+ FDG
Sbjct: 26 TIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFDDPPSAKAAIDWFDG 85
Query: 98 REINGRRVRVEMS 110
+E +G ++V +
Sbjct: 86 KEFSGNPIKVSFA 98
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 29.6 bits (65), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 34/67 (50%), Gaps = 4/67 (5%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGF----VEFEDRRDAEDAVRGFDGREINGRRVR 106
+ DI++ F+ +G +K V + G V FE R DA A++ + G ++GR +
Sbjct: 101 SDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMD 160
Query: 107 VEMSNPQ 113
+++ Q
Sbjct: 161 IQLVASQ 167
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.6 bits (65), Expect = 2.3, Method: Composition-based stats.
Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 5/53 (9%)
Query: 59 FSYYGPIKNVWV----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
FS GP K+ + N P + FVEF + RDA A+ +GR+I G+ V+V
Sbjct: 36 FSQIGPCKSCKMITEHTSNDP-YCFVEFYEHRDAAAALAAMNGRKILGKEVKV 87
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 29.3 bits (64), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 28/57 (49%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRV 107
T++++++ F I+ V G ++EF+ DAE G EI+GR + +
Sbjct: 106 TQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISL 162
>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 = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 31/62 (50%)
Query: 46 CSTSSTKEDIEDAFSYYGPIKNVWVARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRRV 105
S + T++++++ F I+ V G ++EF+ DAE + G EI+GR V
Sbjct: 107 LSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSV 166
Query: 106 RV 107
+
Sbjct: 167 SL 168
>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 = 29.3 bits (64), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 39 IYVSIVLCSTSSTKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVR 93
IYV V +T E++E F G + V + + +P GF ++EF D+ ++
Sbjct: 8 IYVGNV--DYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL- 64
Query: 94 GFDGREINGRRVRV 107
D GR+++V
Sbjct: 65 ALDESLFRGRQIKV 78
>pdb|2CQF|A Chain A, Solution Structure Of The Zinc-Finger Domain In Lin-28
Length = 63
Score = 29.3 bits (64), Expect = 2.8, Method: Composition-based stats.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 219 DKCYECGGRGHYARDCXXXXXXXXXXXXXAVSHAEVAPC 257
D+CY CGG H+A++C ++SH VA C
Sbjct: 8 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHM-VASC 45
Score = 28.5 bits (62), Expect = 4.8, Method: Composition-based stats.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 144 DKCYECGGRGHYARDC 159
D+CY CGG H+A++C
Sbjct: 8 DRCYNCGGLDHHAKEC 23
>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 = 28.9 bits (63), Expect = 4.0, Method: Composition-based stats.
Identities = 16/63 (25%), Positives = 31/63 (49%), Gaps = 6/63 (9%)
Query: 50 STKEDIEDAFSYYGPIKNVWV-----ARNPPGFGFVEFEDRRDAEDAVRGFDGREINGRR 104
+T E++E F G + V + + +P GF ++EF D+ ++ D GR+
Sbjct: 18 ATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-ALDESLFRGRQ 76
Query: 105 VRV 107
++V
Sbjct: 77 IKV 79
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 28.9 bits (63), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 4/60 (6%)
Query: 54 DIEDAFSYYGPIKNVWVARNPPGFGF----VEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
DI++ F+ +G +K V + G V FE + DA A + ++G ++GR +++
Sbjct: 45 DIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGVPLDGRPXNIQL 104
>pdb|2LI8|A Chain A, The Solution Structure Of The Lin28-Znf Domains Bound To
Aggagau Of Pre-Let-7 Mirna
Length = 74
Score = 28.5 bits (62), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 219 DKCYECGGRGHYARDCXXXXXXXXXXXXXAVSHAEVAPC 257
D+CY CGG H+A++C ++SH VA C
Sbjct: 25 DRCYNCGGLDHHAKECKLPPQPKKCHFCQSISHM-VASC 62
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 144 DKCYECGGRGHYARDC 159
D+CY CGG H+A++C
Sbjct: 25 DRCYNCGGLDHHAKEC 40
>pdb|3TRZ|A Chain A, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|B Chain B, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|C Chain C, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|D Chain D, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|E Chain E, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TRZ|F Chain F, Mouse Lin28a In Complex With Let-7d Microrna Pre-Element
pdb|3TS2|A Chain A, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
pdb|3TS2|B Chain B, Mouse Lin28a In Complex With Let-7g Microrna Pre-Element
Length = 148
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 144 DKCYECGGRGHYARDC 159
D+CY CGG H+A++C
Sbjct: 98 DRCYNCGGLDHHAKEC 113
Score = 28.5 bits (62), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 219 DKCYECGGRGHYARDC 234
D+CY CGG H+A++C
Sbjct: 98 DRCYNCGGLDHHAKEC 113
>pdb|3TS0|A Chain A, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
pdb|3TS0|B Chain B, Mouse Lin28a In Complex With Let-7f-1 Microrna Pre-Element
Length = 146
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 144 DKCYECGGRGHYARDC 159
D+CY CGG H+A++C
Sbjct: 96 DRCYNCGGLDHHAKEC 111
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 219 DKCYECGGRGHYARDC 234
D+CY CGG H+A++C
Sbjct: 96 DRCYNCGGLDHHAKEC 111
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
In Daz-Associated Protein 1
Length = 105
Score = 28.5 bits (62), Expect = 5.2, Method: Compositional matrix adjust.
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 5/41 (12%)
Query: 49 SSTKEDIEDAFSYYGPIKNVWVARNPP-----GFGFVEFED 84
S+T+E + FS YG + + + ++ GFGFV+F+D
Sbjct: 27 STTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKD 67
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 28.1 bits (61), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNP 112
GF +E+E AE+A + DG + G +RV P
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNP 112
GF +E+E AE+A + DG + G +RV P
Sbjct: 227 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 263
>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 = 28.1 bits (61), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 76 GFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEMSNP 112
GF +E+E AE+A + DG + G +RV P
Sbjct: 225 GFAVLEYETAEMAEEAQQQADGLSLGGSHLRVSFCAP 261
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.1 bits (61), Expect = 6.5, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 3/61 (4%)
Query: 53 EDIEDAFSYYGPIKNVWVARN---PPGFGFVEFEDRRDAEDAVRGFDGREINGRRVRVEM 109
E + AFS +G I + V GFGFV F +A AV +GR + + + V +
Sbjct: 30 ERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVAL 89
Query: 110 S 110
+
Sbjct: 90 A 90
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 27.3 bits (59), Expect = 9.7, Method: Composition-based stats.
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 4/46 (8%)
Query: 51 TKEDIEDAFSYYGPIKNVWVARNP----PGFGFVEFEDRRDAEDAV 92
T ED+ F +G I V R P G FV+F+ +A+ A+
Sbjct: 25 TDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAI 70
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.321 0.138 0.443
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,751,668
Number of Sequences: 62578
Number of extensions: 255623
Number of successful extensions: 646
Number of sequences better than 100.0: 133
Number of HSP's better than 100.0 without gapping: 99
Number of HSP's successfully gapped in prelim test: 34
Number of HSP's that attempted gapping in prelim test: 487
Number of HSP's gapped (non-prelim): 169
length of query: 312
length of database: 14,973,337
effective HSP length: 99
effective length of query: 213
effective length of database: 8,778,115
effective search space: 1869738495
effective search space used: 1869738495
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)