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= psy4990
(130 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 = 143 bits (361), Expect = 2e-35, Method: Compositional matrix adjust.
Identities = 65/80 (81%), Positives = 73/80 (91%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKA 63
S V+D EMQEHYD FFE+VF E E+KYGE+EEMNVCDNLGDHLVGNVY+KFRREEDAEKA
Sbjct: 25 SAVSDVEMQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKA 84
Query: 64 VNDLNNRWFGGRPVYAELSP 83
V DLNNRWF G+P++AELSP
Sbjct: 85 VIDLNNRWFNGQPIHAELSP 104
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
Specific Factor 1 Variant
Length = 112
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
ED+ VEC K+G+I ++ + D H G + FR E+A+ + L+ RWFGGR + A
Sbjct: 41 EDLRVECS-KFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Query: 80 E 80
+
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 = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 25 ECEDKYGEIEEMNVCDNLG--DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
ECE KYG++ + + + G D ++++F R E A KAV DLN R+FGGR V A
Sbjct: 33 ECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFY 91
Query: 83 PVTDFR 88
+ FR
Sbjct: 92 NLDKFR 97
>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 = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
+DV EC +K+G + + V N GNVY+K A AVN L+ RWF G+ + A
Sbjct: 32 DDVIEEC-NKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWFAGKXITA 87
Query: 80 ELSPVTDFR 88
P+ +
Sbjct: 88 AYVPLPTYH 96
>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 = 0.001, Method: Compositional matrix adjust.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 4/69 (5%)
Query: 20 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 79
+DV EC +K+G + + V N GNVY+K A AVN L+ RWF G+ + A
Sbjct: 31 DDVIEEC-NKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWFAGKMITA 86
Query: 80 ELSPVTDFR 88
P+ +
Sbjct: 87 AYVPLPTYH 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 = 0.004, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 46 LVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 174 IIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 209
>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 = 0.005, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 46 LVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 70 IIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 105
>pdb|2DNY|A Chain A, Solution Structure Of The Third Rna Binding Domain Of Fbp-
Interacting Repressor, Siahbp1
Length = 119
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 46 LVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 65 IIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 100
>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 = 0.078, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 31 GEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 40 GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
>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 = 0.080, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 1/48 (2%)
Query: 31 GEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 35 GPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 82
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/83 (22%), Positives = 35/83 (42%), Gaps = 2/83 (2%)
Query: 29 KYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFR 88
K+G I E+ + + G +I F DA+ A D+N + G+ + E + F+
Sbjct: 30 KHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKSLHGKAIKVEQAKKPSFQ 89
Query: 89 EACCRQYEMVLETKNADPVCTRE 111
R+ ++N P + E
Sbjct: 90 SGGRRRPPA--SSRNRSPSGSLE 110
>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 = 31.2 bits (69), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
KYG I + N+ D L G ++++ + E+A++A++ LNN
Sbjct: 36 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 77
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 26/42 (61%), Gaps = 1/42 (2%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
KYG I + N+ D L G ++++ + E+A++A++ LNN
Sbjct: 112 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153
>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 = 30.8 bits (68), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 36/83 (43%), Gaps = 9/83 (10%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVE--CED------KYGEIEEMNVCDNLG-DHLVGNVYIKF 54
S+ ++ H+ F D+ E ED +G I + V ++ G ++ F
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSF 64
Query: 55 RREEDAEKAVNDLNNRWFGGRPV 77
+ DAE A+ + +W GGR +
Sbjct: 65 FNKWDAENAIQQMGGQWLGGRQI 87
>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 = 30.8 bits (68), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 29 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW--FGGRPVYAELS 82
KYG I + N+ D L G ++++ + E+A++A++ LNN G +P+ L+
Sbjct: 123 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 179
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 30.8 bits (68), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 34/81 (41%), Gaps = 11/81 (13%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 60
+++SN++ +E FE + V N G +I+F EDA
Sbjct: 18 LVLSNLSYSATEETLQEVFEKATF-----------IKVPQNQNGKSKGYAFIEFASFEDA 66
Query: 61 EKAVNDLNNRWFGGRPVYAEL 81
++A+N N R GR + EL
Sbjct: 67 KEALNSCNKREIEGRAIRLEL 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 = 30.4 bits (67), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 16 DNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
N +D GE+E + D + H +G ++ + +DAE+A+N LN
Sbjct: 14 QNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN 67
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 30.0 bits (66), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
N +D GE+E + D + H +G ++ + +DAE+A+N LN
Sbjct: 13 NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN 65
>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 = 30.0 bits (66), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
N +D GE+E + D + H +G ++ + +DAE+A+N LN
Sbjct: 13 NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN 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 = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 33/69 (47%), Gaps = 9/69 (13%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREED 59
+I++ + Q+ + F + GE+E + D + H +G ++ + +D
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSI--------GEVESAKLIRDKVAGHSLGYGFVNYVTAKD 73
Query: 60 AEKAVNDLN 68
AE+A+N LN
Sbjct: 74 AERAINTLN 82
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 29.6 bits (65), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 37/83 (44%), Gaps = 9/83 (10%)
Query: 4 SNVTDEEMQEHYDNFFEDVFVE--CED------KYGEIEEMNVCDNLG-DHLVGNVYIKF 54
S+ ++ H+ F D+ E ED +G+I + V ++ G ++ F
Sbjct: 5 SSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSF 64
Query: 55 RREEDAEKAVNDLNNRWFGGRPV 77
+ DAE A+ + +W GGR +
Sbjct: 65 YNKLDAENAIVHMGGQWLGGRQI 87
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.6 bits (65), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 28 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
++YG + E CD + D+ ++ R EDA +A+ L+N F G+ ++ +LS
Sbjct: 32 EEYGPVIE---CDIVKDY----AFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>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 = 29.3 bits (64), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 30 YGEIEEMNVCDNLG-DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
+G I + V ++ G ++ F + DAE A+ + +W GGR +
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The
C-Fos Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The
Tumor Necrosis Factor Alpha Rna
Length = 167
Score = 29.3 bits (64), Expect = 0.61, Method: Compositional matrix adjust.
Identities = 18/70 (25%), Positives = 33/70 (47%), Gaps = 9/70 (12%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREED 59
+I++ + QE + + F + GEIE + D + +G ++ + +D
Sbjct: 5 LIVNYLPQNMTQEEFRSLFGSI--------GEIESCKLVRDKITGQSLGYGFVNYIDPKD 56
Query: 60 AEKAVNDLNN 69
AEKA+N LN
Sbjct: 57 AEKAINTLNG 66
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 29.3 bits (64), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 16/85 (18%)
Query: 1 MIISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRR 56
+++SN V+D ++QE +F E +G +++ V + +G + F R
Sbjct: 31 LLVSNLDFGVSDADIQE--------LFAE----FGTLKKAAVHYDRSGRSLGTADVHFER 78
Query: 57 EEDAEKAVNDLNNRWFGGRPVYAEL 81
+ DA KA+ N GRP+ +L
Sbjct: 79 KADALKAMKQYNGVPLDGRPMNIQL 103
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 17 NFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV-GNVYIKFRREEDAEKAVNDLNNRWFGG 74
N +D +E YG+I+ +++ + + HL G Y++F ++AEKA+ ++ G
Sbjct: 15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
Query: 75 RPVYAE--LSP 83
+ + A L+P
Sbjct: 75 QEITATAVLAP 85
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 28.9 bits (63), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 43 GDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
G G ++ F E+A KAV ++N R +P+Y L+
Sbjct: 51 GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALA 90
>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 = 1.1, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 35 EMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
+ N+ D L+ ++IK D K ++++ + FGG P+Y L
Sbjct: 299 DKNITDKFAQELIDCIWIKL---NDINKVRDEISTKHFGGYPMYQNL 342
>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 = 1.4, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 28 DKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNN 69
++YG IE + VCD G ++KF+ A++A+ LN
Sbjct: 64 ERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLNG 106
>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 = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 24 VECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 83
+ C DK + ++ NL D L+ + I+ R D ++++ NRW+ +++ S
Sbjct: 4 LNCHDKCSTTTQSDI--NLKDELLSSTSIECRPGNDLLESLHKEQNRWYSETKTFSDSSQ 61
Query: 84 VT 85
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 = 27.7 bits (60), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 16/85 (18%)
Query: 1 MIISN----VTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRR 56
+++SN V+D ++QE +F E +G +++ V + +G + F R
Sbjct: 32 LLVSNLDFGVSDADIQE--------LFAE----FGTLKKAAVHYDRSGRSLGTADVHFER 79
Query: 57 EEDAEKAVNDLNNRWFGGRPVYAEL 81
+ DA KA N GRP +L
Sbjct: 80 KADALKAXKQYNGVPLDGRPXNIQL 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 = 27.7 bits (60), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 32/79 (40%), Gaps = 5/79 (6%)
Query: 38 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREA--CCRQY 95
VCD G G ++ F +E AE+A+ +N R V+ REA R
Sbjct: 38 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAK 95
Query: 96 EMV-LETKNADPVCTREKA 113
E + KN P TR A
Sbjct: 96 EFTNVYIKNFGPGSTRAAA 114
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 26.9 bits (58), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
N +D F G+IE + D + +G ++ + DA+KA+N LN
Sbjct: 15 NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLN 67
>pdb|4IG8|A Chain A, Structural Basis For Cytosolic Double-stranded Rna
Surveillance By Human Oas1
Length = 349
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 81 LSPVTDFREACCRQYEMVLETKNADPVCTREKA 113
LSP+T F++ R+ E + E + C RE+A
Sbjct: 82 LSPLTTFQDQLNRRGEFIQEIRRQLEACQRERA 114
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 17 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 68
N +D F G+IE + D + +G ++ + DA+KA+N LN
Sbjct: 15 NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLN 67
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 26.6 bits (57), Expect = 3.8, Method: Compositional matrix adjust.
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 49 NVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 81
+ Y+ + R EDA +A+ +NN GR + A L
Sbjct: 65 SAYVTYIRSEDALRAIQCVNNVVVDGRTLKASL 97
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 16/69 (23%), Positives = 32/69 (46%), Gaps = 12/69 (17%)
Query: 1 MIISNVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDA 60
M+ TDE++++ ++ F G I+E V G ++KF+ +A
Sbjct: 19 MLGKQQTDEDVRKMFEPF------------GTIDECTVLRGPDGTSKGCAFVKFQTHAEA 66
Query: 61 EKAVNDLNN 69
+ A+N L++
Sbjct: 67 QAAINTLHS 75
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 26.6 bits (57), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 16/73 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N+T++E++E +++ E V + K G YI+F+ E DAEK +
Sbjct: 27 NITEDELKEVFEDALEIRLVSQDGKS----------------KGIAYIEFKSEADAEKNL 70
Query: 65 NDLNNRWFGGRPV 77
+ GR V
Sbjct: 71 EEKQGAEIDGRSV 83
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G + F ++A AV DLN+R G R V
Sbjct: 58 GEAMVAFESRDEATAAVIDLNDRPIGSRKV 87
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 26.2 bits (56), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G + F ++A AV DLN+R G R V
Sbjct: 58 GEAMVAFESRDEATAAVIDLNDRPIGSRKV 87
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 50 VYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTD 86
++ F EDA +A+ LN + G P+ L+ D
Sbjct: 54 AFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 90
>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 = 25.8 bits (55), Expect = 6.1, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 32 EIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
E+E N D+LG + R +E+ E+ +N+L R P+
Sbjct: 158 EVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDNPI 203
>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 = 25.8 bits (55), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 16/73 (21%)
Query: 5 NVTDEEMQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAV 64
N+T++E++E +++ E V + K G YI+F+ E DAEK +
Sbjct: 110 NITEDELKEVFEDALEIRLVSQDGKSK----------------GIAYIEFKSEADAEKNL 153
Query: 65 NDLNNRWFGGRPV 77
+ GR V
Sbjct: 154 EEKQGAEIDGRSV 166
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 25.8 bits (55), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 48 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 77
G + F ++A AV DLN+R G R V
Sbjct: 58 GEAXVAFESRDEATAAVIDLNDRPIGSRKV 87
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 25.4 bits (54), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 39 CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 82
CD + D+ ++ +E DA+ A+ LN + G+ + ELS
Sbjct: 39 CDVVKDY----AFVHMEKEADAKAAIAQLNGKEVKGKRINVELS 78
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
0.317 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,947,295
Number of Sequences: 62578
Number of extensions: 159593
Number of successful extensions: 412
Number of sequences better than 100.0: 51
Number of HSP's better than 100.0 without gapping: 34
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 370
Number of HSP's gapped (non-prelim): 59
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)