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= psy12245
(189 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 173 bits (439), Expect = 5e-44, Method: Compositional matrix adjust.
Identities = 83/106 (78%), Positives = 94/106 (88%), Gaps = 2/106 (1%)
Query: 28 SQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMN 87
SQTI LLN+Y NPQNS++SADG L S V+D EMQEHYD FFE+VF E E+KYGE+EEMN
Sbjct: 1 SQTIALLNIYRNPQNSSQSADG--LRSAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMN 58
Query: 88 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
VCDNLGDHLVGNVY+KFRREEDAEKAV DLNNRWF G+P++AELSP
Sbjct: 59 VCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 43.9 bits (102), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 70 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 129
ED+ VEC K+G+I ++ + D H G + FR E+A+ + L+ RWFGGR + A
Sbjct: 41 EDLRVECS-KFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Query: 130 E 130
+
Sbjct: 97 Q 97
>pdb|2PE8|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 (free
Form)
pdb|2PEH|A Chain A, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
pdb|2PEH|B Chain B, Crystal Structure Of The Uhm Domain Of Human Spf45 In
Complex With Sf3b155-Ulm5
Length = 105
Score = 40.4 bits (93), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 75 ECEDKYGEIEEMNVCDNLG--DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
ECE KYG++ + + + G D ++++F R E A KAV DLN R+FGGR V A
Sbjct: 33 ECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFY 91
Query: 133 PVTDFR 138
+ FR
Sbjct: 92 NLDKFR 97
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From Mus
Musculus
Length = 113
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/88 (30%), Positives = 45/88 (51%), Gaps = 5/88 (5%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
S++ + T+EE+ +D +D +E +K+G + + V N GNVY+K
Sbjct: 12 SNMFNPQTEEEVG--WDTEIKDDVIEECNKHGGVIHIYVDKNSAQ---GNVYVKCPSIAA 66
Query: 110 AEKAVNDLNNRWFGGRPVYAELSPVTDF 137
A AVN L+ RWF G+ + A P+ +
Sbjct: 67 AIAAVNALHGRWFAGKMITAAYVPLPTY 94
>pdb|3S6E|A Chain A, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
pdb|3S6E|B Chain B, Crystal Structure Of A Rna Binding Motif Protein 39
(Rbm39) From Mus Musculus At 0.95 A Resolution
Length = 114
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 41/81 (50%), Gaps = 5/81 (6%)
Query: 57 TDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVND 116
T+EE+ +D +D +E +K+G + + V N GNVY+K A AVN
Sbjct: 20 TEEEVG--WDTEIKDDVIEECNKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNA 74
Query: 117 LNNRWFGGRPVYAELSPVTDF 137
L+ RWF G+ + A P+ +
Sbjct: 75 LHGRWFAGKXITAAYVPLPTY 95
>pdb|3DXB|A Chain A, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|B Chain B, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|C Chain C, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|D Chain D, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|E Chain E, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|F Chain F, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|G Chain G, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
pdb|3DXB|H Chain H, Structure Of The Uhm Domain Of Puf60 Fused To Thioredoxin
Length = 222
Score = 36.6 bits (83), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 95 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 173 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 209
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 36.6 bits (83), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 95 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 64 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 100
>pdb|3UE2|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.23 A Resolution
pdb|3US5|A Chain A, Crystal Structure Of A Rna-Binding Domain Of A Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 1.38 A Resolution
Length = 118
Score = 36.2 bits (82), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 95 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 69 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 32.7 bits (73), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 4/92 (4%)
Query: 62 QEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW 121
+E + + VF K+G I E+ + + G +I F DA+ A D+N +
Sbjct: 17 RETNEKMLKAVF----GKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKS 72
Query: 122 FGGRPVYAELSPVTDFREACCRQYEMGECTRS 153
G+ + E + F+ R+ RS
Sbjct: 73 LHGKAIKVEQAKKPSFQSGGRRRPPASSRNRS 104
>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 = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 70 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
E + E G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 29 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
Score = 26.6 bits (57), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 88 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 147
VCD G G ++ F +E AE+A+ +N R V+ V F+ R+ E+
Sbjct: 136 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAEL 188
Query: 148 G 148
G
Sbjct: 189 G 189
>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 = 32.3 bits (72), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 70 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
E + E G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 24 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 82
Score = 26.9 bits (58), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 88 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 147
VCD G G ++ F +E AE+A+ +N R V+ V F+ R+ E+
Sbjct: 131 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAEL 183
Query: 148 G 148
G
Sbjct: 184 G 184
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 32.0 bits (71), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 15/86 (17%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREE 108
++L +TD+++ D F KYG I + N+ D L G ++++ + E
Sbjct: 95 TNLPRTITDDQL----DTIF--------GKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 142
Query: 109 DAEKAVNDLNNRW--FGGRPVYAELS 132
+A++A++ LNN G +P+ L+
Sbjct: 143 EAQEAISALNNVIPEGGSQPLSVRLA 168
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 31.6 bits (70), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 37/71 (52%), Gaps = 13/71 (18%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREE 108
++L +TD+++ D F KYG I + N+ D L G ++++ + E
Sbjct: 19 TNLPRTITDDQL----DTIF--------GKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 66
Query: 109 DAEKAVNDLNN 119
+A++A++ LNN
Sbjct: 67 EAQEAISALNN 77
>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 = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 22/86 (25%), Positives = 43/86 (50%), Gaps = 15/86 (17%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREE 108
++L +TD+++ D F KYG I + N+ D L G ++++ + E
Sbjct: 106 TNLPRTITDDQL----DTIF--------GKYGSIVQKNILRDKLTGRPRGVAFVRYNKRE 153
Query: 109 DAEKAVNDLNNRW--FGGRPVYAELS 132
+A++A++ LNN G +P+ L+
Sbjct: 154 EAQEAISALNNVIPEGGSQPLSVRLA 179
>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 = 30.8 bits (68), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 50 SHLISNVTDEEM-QEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRRE 107
++LI N + M Q+ + F + GE+E + D + H +G ++ +
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSI--------GEVESAKLIRDKVAGHSLGYGFVNYVTA 56
Query: 108 EDAEKAVNDLN 118
+DAE+A+N LN
Sbjct: 57 KDAERAINTLN 67
>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 = 30.4 bits (67), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 54 SNVTDEEMQEHYDNFFEDVFVE--CED------KYGEIEEMNVCDNLG-DHLVGNVYIKF 104
S+ ++ H+ F D+ E ED +G I + V ++ G ++ F
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 105 RREEDAEKAVNDLNNRWFGGRPV 127
+ DAE A+ + +W GGR +
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQI 87
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 30.4 bits (67), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 13/69 (18%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREED 109
+L N+T +E++ + + GE+E + D + H +G ++ + +D
Sbjct: 9 YLPQNMTQDELRSLFSSI------------GEVESAKLIRDKVAGHSLGYGFVNYVTAKD 56
Query: 110 AEKAVNDLN 118
AE+A+N LN
Sbjct: 57 AERAINTLN 65
>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 = 30.4 bits (67), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 10/72 (13%)
Query: 49 GSHLISN-VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRR 106
G++LI N + Q+ + F + GE+E + D + H +G ++ +
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSI--------GEVESAKLIRDKVAGHSLGYGFVNYVT 70
Query: 107 EEDAEKAVNDLN 118
+DAE+A+N LN
Sbjct: 71 AKDAERAINTLN 82
>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 = 30.4 bits (67), Expect = 0.63, Method: Compositional matrix adjust.
Identities = 17/69 (24%), Positives = 34/69 (49%), Gaps = 13/69 (18%)
Query: 51 HLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREED 109
+L N+T +E++ + + GE+E + D + H +G ++ + +D
Sbjct: 9 YLPQNMTQDELRSLFSSI------------GEVESAKLIRDKVAGHSLGYGFVNYVTAKD 56
Query: 110 AEKAVNDLN 118
AE+A+N LN
Sbjct: 57 AERAINTLN 65
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 30.4 bits (67), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 28/127 (22%), Positives = 49/127 (38%), Gaps = 34/127 (26%)
Query: 14 HGDRCSRIHNKPTFSQTILLLNLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVF 73
GDR +R ++NLY+ +L + DE +++ + F
Sbjct: 6 SGDRITRYQ----------VVNLYVK-----------NLDDGIDDERLRKAFSPF----- 39
Query: 74 VECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
G I V G G ++ F E+A KAV ++N R +P+Y L+
Sbjct: 40 -------GTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQ 91
Query: 134 VTDFREA 140
+ R++
Sbjct: 92 RKEERQS 98
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 30.0 bits (66), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 78 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 132
++YG + E CD + D+ ++ R EDA +A+ L+N F G+ ++ +LS
Sbjct: 32 EEYGPVIE---CDIVKDY----AFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.0 bits (66), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 23/82 (28%), Positives = 38/82 (46%), Gaps = 15/82 (18%)
Query: 50 SHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREED 109
S+L + T+E +QE ++ + F++ V N G +I+F ED
Sbjct: 21 SNLSYSATEETLQEVFE---KATFIK------------VPQNQNGKSKGYAFIEFASFED 65
Query: 110 AEKAVNDLNNRWFGGRPVYAEL 131
A++A+N N R GR + EL
Sbjct: 66 AKEALNSCNKREIEGRAIRLEL 87
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 30.0 bits (66), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 9/83 (10%)
Query: 54 SNVTDEEMQEHYDNFFEDVFVE--CED------KYGEIEEMNVCDNLG-DHLVGNVYIKF 104
S+ ++ H+ F D+ E ED +G+I + V ++ G ++ F
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Query: 105 RREEDAEKAVNDLNNRWFGGRPV 127
+ DAE A+ + +W GGR +
Sbjct: 65 YNKLDAENAIVHMGGQWLGGRQI 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 = 29.6 bits (65), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 80 YGEIEEMNVCDNLG-DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
+G I + V ++ G ++ F + DAE A+ + +W GGR +
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|1TLA|A Chain A, Hydrophobic Core Repacking And Aromatic-Aromatic
Interaction In The Thermostable Mutant Of T4 Lysozyme
Ser 117 (Right Arrow) Phe
Length = 164
Score = 29.6 bits (65), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 129 AELSPVTDFREACCRQ------YEMGECTRSGFCNFMHL 161
A+L PV D +A R ++MGE +GF NF+ +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNFLRM 120
>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 = 29.6 bits (65), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 35/71 (49%), Gaps = 10/71 (14%)
Query: 50 SHLISNVTDEEM-QEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRRE 107
++LI N + M QE + + F + GEIE + D + +G ++ +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSI--------GEIESCKLVRDKITGQSLGYGFVNYIDP 54
Query: 108 EDAEKAVNDLN 118
+DAEKA+N LN
Sbjct: 55 KDAEKAINTLN 65
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 29.3 bits (64), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 39/84 (46%), Gaps = 16/84 (19%)
Query: 52 LISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 107
L+SN V+D ++QE +F E +G +++ V + +G + F R+
Sbjct: 32 LVSNLDFGVSDADIQE--------LFAE----FGTLKKAAVHYDRSGRSLGTADVHFERK 79
Query: 108 EDAEKAVNDLNNRWFGGRPVYAEL 131
DA KA+ N GRP+ +L
Sbjct: 80 ADALKAMKQYNGVPLDGRPMNIQL 103
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/65 (26%), Positives = 35/65 (53%), Gaps = 2/65 (3%)
Query: 67 NFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV-GNVYIKFRREEDAEKAVNDLNNRWFGG 124
N +D +E YG+I+ +++ + + HL G Y++F ++AEKA+ ++ G
Sbjct: 15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
Query: 125 RPVYA 129
+ + A
Sbjct: 75 QEITA 79
>pdb|2IGC|A Chain A, Structure Of Spin Labeled T4 Lysozyme Mutant T115r1a
pdb|2NTG|A Chain A, Structure Of Spin-Labeled T4 Lysozyme Mutant T115r7
pdb|2OU8|A Chain A, Structure Of Spin-Labeled T4 Lysozyme Mutant T115r1 At
Room Temperature
Length = 164
Score = 28.9 bits (63), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 129 AELSPVTDFREACCRQ------YEMGECTRSGFCNFMHL 161
A+L PV D +A R ++MGE +GFCN + +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFCNSLRM 120
>pdb|2OU9|A Chain A, Structure Of Spin-Labeled T4 Lysozyme Mutant T115r1R119A
Length = 164
Score = 28.5 bits (62), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 129 AELSPVTDFREACCRQ------YEMGECTRSGFCNFMHL 161
A+L PV D +A R ++MGE +GFCN + +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFCNSLAM 120
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 16/85 (18%)
Query: 43 SAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYI 102
+A++ +L N+T++E++E +++ E V + K G YI
Sbjct: 15 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK----------------GIAYI 58
Query: 103 KFRREEDAEKAVNDLNNRWFGGRPV 127
+F+ E DAEK + + GR V
Sbjct: 59 EFKSEADAEKNLEEKQGAEIDGRSV 83
>pdb|1R8W|A Chain A, Native Structure Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R8W|B Chain B, Native Structure Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9D|A Chain A, Glycerol Bound Form Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9D|B Chain B, Glycerol Bound Form Of The B12-Independent Glycerol
Dehydratase From Clostridium Butyricum
pdb|1R9E|A Chain A, Structure Of The B12-Independent Glycerol Dehydratase With
1,2-Propanediol Bound
pdb|1R9E|B Chain B, Structure Of The B12-Independent Glycerol Dehydratase With
1,2-Propanediol Bound
Length = 787
Score = 28.5 bits (62), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 87 NVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 131
N+ D L+ ++IK D K ++++ + FGG P+Y L
Sbjct: 301 NITDKFAQELIDCIWIKLN---DINKVRDEISTKHFGGYPMYQNL 342
>pdb|1K8K|F Chain F, Crystal Structure Of Arp23 COMPLEX
pdb|1TYQ|F Chain F, Crystal Structure Of Arp23 COMPLEX WITH BOUND ATP AND
Calcium
pdb|1U2V|F Chain F, Crystal Structure Of Arp23 COMPLEX WITH BOUND ADP AND
Calcium
pdb|2P9I|F Chain F, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp And Crosslinked With Gluteraldehyde
pdb|2P9K|F Chain F, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Atp And Crosslinked With Glutaraldehyde
pdb|2P9L|F Chain F, Crystal Structure Of Bovine Arp23 COMPLEX
pdb|2P9N|F Chain F, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp
pdb|2P9P|F Chain F, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Adp
pdb|2P9S|F Chain F, Structure Of Bovine Arp23 COMPLEX CO-Crystallized With
AtpMG2+
pdb|2P9U|F Chain F, Crystal Structure Of Bovine Arp23 COMPLEX CO-Crystallized
With Amp-Pnp And Calcium
pdb|3DXK|F Chain F, Structure Of Bos Taurus Arp23 COMPLEX WITH BOUND INHIBITOR
Ck0944636
pdb|3DXM|F Chain F, Structure Of Bos Taurus Arp23 COMPLEX WITH BOUND INHIBITOR
Ck0993548
pdb|3RSE|F Chain F, Structural And Biochemical Characterization Of Two Binding
Sites For Nucleation Promoting Factor Wasp-Vca On Arp23
COMPLEX
pdb|3UKR|F Chain F, Crystal Structure Of Bos Taurus Arp2/3 Complex With Bound
Inhibitor Ck-666
pdb|3UKU|F Chain F, Structure Of Arp2/3 Complex With Bound Inhibitor Ck-869
pdb|3ULE|F Chain F, Structure Of Bos Taurus Arp2/3 Complex With Bound
Inhibitor Ck-869 And Atp
Length = 168
Score = 28.1 bits (61), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 2/69 (2%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGD 94
N +I + + D S LI+N E+M +H F F+E DK EI EM + N
Sbjct: 100 NFFILRRKPVEGYDISFLITNFHTEQMYKHKLVDFVIHFMEEIDK--EISEMKLSVNARA 157
Query: 95 HLVGNVYIK 103
+V ++K
Sbjct: 158 RIVAEEFLK 166
>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 = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 21/85 (24%), Positives = 38/85 (44%), Gaps = 16/85 (18%)
Query: 43 SAKSADGSHLISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYI 102
+A++ +L N+T++E++E +++ E V + K G YI
Sbjct: 98 AARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSK----------------GIAYI 141
Query: 103 KFRREEDAEKAVNDLNNRWFGGRPV 127
+F+ E DAEK + + GR V
Sbjct: 142 EFKSEADAEKNLEEKQGAEIDGRSV 166
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 28.1 bits (61), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 78 DKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 119
++YG IE + VCD G ++KF+ A++A+ LN
Sbjct: 64 ERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>pdb|3L2X|A Chain A, Crystal Structure Of Spin Labeled T4 Lysozyme Mutant
115-119rx
Length = 164
Score = 27.7 bits (60), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 129 AELSPVTDFREACCRQ------YEMGECTRSGFCNFM 159
A+L PV D +A R ++MGE +GFCN +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFCNSL 118
>pdb|3G8L|A Chain A, Crystal Structure Of Murine Natural Killer Cell Receptor,
Ly49l4
pdb|3G8L|B Chain B, Crystal Structure Of Murine Natural Killer Cell Receptor,
Ly49l4
pdb|3G8L|C Chain C, Crystal Structure Of Murine Natural Killer Cell Receptor,
Ly49l4
pdb|3G8L|D Chain D, Crystal Structure Of Murine Natural Killer Cell Receptor,
Ly49l4
Length = 190
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 74 VECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 133
+ C DK + ++ NL D L+ + I+ R D ++++ NRW+ +++ S
Sbjct: 4 LNCHDKCSTTTQSDI--NLKDELLSSTSIECRPGNDLLESLHKEQNRWYSETKTFSDSSQ 61
Query: 134 VT 135
T
Sbjct: 62 HT 63
>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 = 27.3 bits (59), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 16/84 (19%)
Query: 52 LISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRRE 107
L+SN V+D ++QE +F E +G +++ V + +G + F R+
Sbjct: 33 LVSNLDFGVSDADIQE--------LFAE----FGTLKKAAVHYDRSGRSLGTADVHFERK 80
Query: 108 EDAEKAVNDLNNRWFGGRPVYAEL 131
DA KA N GRP +L
Sbjct: 81 ADALKAXKQYNGVPLDGRPXNIQL 104
>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 = 27.3 bits (59), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 88 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 147
VCD G G ++ F +E AE+A+ +N R V+ V F+ R+ E+
Sbjct: 38 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAEL 90
Query: 148 G 148
G
Sbjct: 91 G 91
>pdb|2ZUE|A Chain A, Crystal Structure Of Pyrococcus Horikoshii Arginyl-Trna
Synthetase Complexed With Trna(Arg) And An Atp Analog
(Anp)
pdb|2ZUF|A Chain A, Crystal Structure Of Pyrococcus Horikoshii Arginyl-Trna
Synthetase Complexed With Trna(Arg)
Length = 629
Score = 26.9 bits (58), Expect = 7.4, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 82 EIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 127
E+E N D+LG + R +E+ E+ +N+L R P+
Sbjct: 158 EVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDNPI 203
>pdb|3FW2|A Chain A, C-Terminal Domain Of Putative Thiol-Disulfide
Oxidoreductase From Bacteroides Thetaiotaomicron.
pdb|3FW2|B Chain B, C-Terminal Domain Of Putative Thiol-Disulfide
Oxidoreductase From Bacteroides Thetaiotaomicron.
pdb|3FW2|C Chain C, C-Terminal Domain Of Putative Thiol-Disulfide
Oxidoreductase From Bacteroides Thetaiotaomicron.
pdb|3FW2|D Chain D, C-Terminal Domain Of Putative Thiol-Disulfide
Oxidoreductase From Bacteroides Thetaiotaomicron
Length = 150
Score = 26.6 bits (57), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 21/38 (55%)
Query: 35 NLYINPQNSAKSADGSHLISNVTDEEMQEHYDNFFEDV 72
++Y P N S+DG L N+ EE+++ +N E+
Sbjct: 113 SIYKIPANILLSSDGKILAKNLRGEELKKKIENIVEEA 150
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
0.322 0.139 0.441
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,201,297
Number of Sequences: 62578
Number of extensions: 212759
Number of successful extensions: 494
Number of sequences better than 100.0: 44
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 459
Number of HSP's gapped (non-prelim): 53
length of query: 189
length of database: 14,973,337
effective HSP length: 93
effective length of query: 96
effective length of database: 9,153,583
effective search space: 878743968
effective search space used: 878743968
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: 48 (23.1 bits)