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= psy17806
(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 = 135 bits (341), Expect = 5e-33, Method: Compositional matrix adjust.
Identities = 61/73 (83%), Positives = 68/73 (93%)
Query: 1 MQEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNR 60
MQEHYD FFE+VF E E+KYGE+EEMNVCDNLGDHLVGNVY+KFRREEDAEKAV DLNNR
Sbjct: 32 MQEHYDEFFEEVFTEMEEKYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNR 91
Query: 61 WFGGRPVYAELSP 73
WF G+P++AELSP
Sbjct: 92 WFNGQPIHAELSP 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 = 3e-05, Method: Compositional matrix adjust.
Identities = 23/61 (37%), Positives = 36/61 (59%), Gaps = 4/61 (6%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
ED+ VEC K+G+I ++ + D H G + FR E+A+ + L+ RWFGGR + A
Sbjct: 41 EDLRVECS-KFGQIRKLLLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGRQITA 96
Query: 70 E 70
+
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 = 40.0 bits (92), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 27/66 (40%), Positives = 38/66 (57%), Gaps = 3/66 (4%)
Query: 15 ECEDKYGEIEEMNVCDNLG--DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
ECE KYG++ + + + G D ++++F R E A KAV DLN R+FGGR V A
Sbjct: 33 ECE-KYGKVGKCVIFEIPGAPDDEAVRIFLEFERVESAIKAVVDLNGRYFGGRVVKACFY 91
Query: 73 PVTDFR 78
+ 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 = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+DV EC +K+G + + V N GNVY+K A AVN L+ RWF G+ + A
Sbjct: 32 DDVIEEC-NKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWFAGKXITA 87
Query: 70 ELSPVTDF 77
P+ +
Sbjct: 88 AYVPLPTY 95
>pdb|2LQ5|A Chain A, Nmr Structure Of The Rna Binding Motif 39 (Rbm39) From
Mus Musculus
Length = 113
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 10 EDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYA 69
+DV EC +K+G + + V N GNVY+K A AVN L+ RWF G+ + A
Sbjct: 31 DDVIEEC-NKHGGVIHIYVDKNSAQ---GNVYVKCPSIAAAIAAVNALHGRWFAGKMITA 86
Query: 70 ELSPVTDF 77
P+ +
Sbjct: 87 AYVPLPTY 94
>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 = 13/37 (35%), Positives = 22/37 (59%)
Query: 35 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 173 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 36 LVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
++ ++++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 = 36.6 bits (83), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 35 HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
++ ++++F + KA+ LN RWF GR V AE+
Sbjct: 64 EIIVKIFVEFSIASETHKAIQALNGRWFAGRKVVAEV 100
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 33.1 bits (74), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 21/92 (22%), Positives = 37/92 (40%), Gaps = 4/92 (4%)
Query: 2 QEHYDNFFEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW 61
+E + + VF K+G I E+ + + G +I F DA+ A D+N +
Sbjct: 17 RETNEKMLKAVF----GKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNGKS 72
Query: 62 FGGRPVYAELSPVTDFREACCRQYEMGECTRS 93
G+ + E + F+ R+ RS
Sbjct: 73 LHGKAIKVEQAKKPSFQSGGRRRPPASSRNRS 104
>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 = 0.071, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
E + E G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 24 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 82
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 28 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 87
VCD G G ++ F +E AE+A+ +N R V+ V F+ R+ E+
Sbjct: 131 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAEL 183
Query: 88 G 88
G
Sbjct: 184 G 184
>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 = 0.073, Method: Compositional matrix adjust.
Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 1/59 (1%)
Query: 10 EDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
E + E G I + VC D + +G Y+ F++ DAE+A++ +N G+PV
Sbjct: 29 EAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFDVIKGKPV 87
Score = 25.8 bits (55), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 28 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 87
VCD G G ++ F +E AE+A+ +N R V+ V F+ R+ E+
Sbjct: 136 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAEL 188
Query: 88 G 88
G
Sbjct: 189 G 189
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 31.6 bits (70), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW--FGGRPVYAELS 72
KYG I + N+ D L G ++++ + E+A++A++ LNN G +P+ L+
Sbjct: 112 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 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 = 0.13, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW--FGGRPVYAELS 72
KYG I + N+ D L G ++++ + E+A++A++ LNN G +P+ L+
Sbjct: 36 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 92
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 31.6 bits (70), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 3/57 (5%)
Query: 19 KYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLNNRW--FGGRPVYAELS 72
KYG I + N+ D L G ++++ + E+A++A++ LNN G +P+ L+
Sbjct: 123 KYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNVIPEGGSQPLSVRLA 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 = 0.20, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 6 DNFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
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 = 30.4 bits (67), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
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 = 30.4 bits (67), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
N +D GE+E + D + H +G ++ + +DAE+A+N LN
Sbjct: 13 NMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN 65
>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 = 29.6 bits (65), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 20 YGEIEEMNVCDNLGD-HLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G I + V ++ G ++ F + DAE A+ + +W GGR +
Sbjct: 39 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 87
>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 = 0.52, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
N +D GE+E + D + H +G ++ + +DAE+A+N LN
Sbjct: 30 NXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTLN 82
>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 = 0.55, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 20 YGEIEEMNVCDNLG-DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G I + V ++ G ++ F + DAE A+ + +W GGR +
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQI 78
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.3 bits (64), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 31/55 (56%), Gaps = 7/55 (12%)
Query: 18 DKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELS 72
++YG + E CD + D+ ++ R EDA +A+ L+N F G+ ++ +LS
Sbjct: 32 EEYGPVIE---CDIVKDY----AFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLS 79
>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 = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 69 AELSPVTDFREACCRQ------YEMGECTRSGFCNFMHL 101
A+L PV D +A R ++MGE +GF NF+ +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNFLRM 120
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 4/71 (5%)
Query: 7 NFFEDVFVECEDKYGEIEEMNV-CDNLGDHLV-GNVYIKFRREEDAEKAVNDLNNRWFGG 64
N +D +E YG+I+ +++ + + HL G Y++F ++AEKA+ ++ G
Sbjct: 15 NVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
Query: 65 RPVYAE--LSP 73
+ + A L+P
Sbjct: 75 QEITATAVLAP 85
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.9 bits (63), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 26 MNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
+ V N G +I+F EDA++A+N N R GR + EL
Sbjct: 42 IKVPQNQNGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL 87
>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 = 28.9 bits (63), Expect = 0.81, Method: Composition-based stats.
Identities = 13/47 (27%), Positives = 24/47 (51%), Gaps = 3/47 (6%)
Query: 25 EMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
+ N+ D L+ ++IK D K ++++ + FGG P+Y L
Sbjct: 299 DKNITDKFAQELIDCIWIKL---NDINKVRDEISTKHFGGYPMYQNL 342
>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 = 0.83, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 29/61 (47%), Gaps = 1/61 (1%)
Query: 20 YGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFRE 79
+G I V G G ++ F E+A KAV ++N R +P+Y L+ + R+
Sbjct: 39 FGTITSAKVMME-GGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQ 97
Query: 80 A 80
+
Sbjct: 98 S 98
>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 = 0.92, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 69 AELSPVTDFREACCRQ------YEMGECTRSGFCNFMHL 101
A+L PV D +A R ++MGE +GFCN + +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFCNSLRM 120
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 28.5 bits (62), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 13/49 (26%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 20 YGEIEEMNVCDNLG-DHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
+G+I + V ++ G ++ F + DAE A+ + +W GGR +
Sbjct: 39 FGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQI 87
>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 = 28.5 bits (62), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/62 (24%), Positives = 30/62 (48%), Gaps = 2/62 (3%)
Query: 14 VECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
+ C DK + ++ NL D L+ + I+ R D ++++ NRW+ +++ S
Sbjct: 4 LNCHDKCSTTTQSDI--NLKDELLSSTSIECRPGNDLLESLHKEQNRWYSETKTFSDSSQ 61
Query: 74 VT 75
T
Sbjct: 62 HT 63
>pdb|2OU9|A Chain A, Structure Of Spin-Labeled T4 Lysozyme Mutant T115r1R119A
Length = 164
Score = 28.1 bits (61), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 6/39 (15%)
Query: 69 AELSPVTDFREACCRQ------YEMGECTRSGFCNFMHL 101
A+L PV D +A R ++MGE +GFCN + +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFCNSLAM 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 = 28.1 bits (61), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 24/48 (50%), Gaps = 4/48 (8%)
Query: 15 ECEDKYGEIEEMNVCDNLGDHLVGNV----YIKFRREEDAEKAVNDLN 58
E +G I E+ C + D + G ++ + +DAEKA+N LN
Sbjct: 18 EFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAINTLN 65
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 27.7 bits (60), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 1/42 (2%)
Query: 18 DKYGEIEEMN-VCDNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
++YG IE + VCD G ++KF+ A++A+ LN
Sbjct: 64 ERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGLN 105
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 27.3 bits (59), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 30/63 (47%), Gaps = 4/63 (6%)
Query: 9 FEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+++F E +G +++ V + +G + F R+ DA KA+ N GRP+
Sbjct: 45 IQELFAE----FGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMN 100
Query: 69 AEL 71
+L
Sbjct: 101 IQL 103
>pdb|3L2X|A Chain A, Crystal Structure Of Spin Labeled T4 Lysozyme Mutant
115-119rx
Length = 164
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 6/37 (16%)
Query: 69 AELSPVTDFREACCRQ------YEMGECTRSGFCNFM 99
A+L PV D +A R ++MGE +GFCN +
Sbjct: 82 AKLKPVYDSLDAVRRAALINMVFQMGETGVAGFCNSL 118
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 27.3 bits (59), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 30/58 (51%), Gaps = 6/58 (10%)
Query: 19 KYGEIEEMNVCDNLGDHL-----VGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAEL 71
K+G+I ++ V +N + + Y+ + R EDA +A+ +NN GR + A L
Sbjct: 41 KFGKIHKV-VINNSTSYAGSQGPSASAYVTYIRSEDALRAIQCVNNVVVDGRTLKASL 97
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 38 GNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
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 = 26.6 bits (57), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 37 VGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
G + F ++A AV DLN+R G R V
Sbjct: 57 TGEAMVAFESRDEATAAVIDLNDRPIGSRKV 87
>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 = 26.6 bits (57), Expect = 4.2, Method: Composition-based stats.
Identities = 13/46 (28%), Positives = 22/46 (47%)
Query: 22 EIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
E+E N D+LG + R +E+ E+ +N+L R P+
Sbjct: 158 EVEVQNYIDDLGIQFAQVYWGYLRLKEEFERIMNELRERGLKDNPI 203
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human
Pabpc1 A Ph 9.0
Length = 115
Score = 26.6 bits (57), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 7/61 (11%)
Query: 28 VCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTDFREACCRQYEM 87
VCD G G ++ F +E AE+A+ +N R V+ V F+ R+ E+
Sbjct: 38 VCDENGSKGYG--FVHFETQEAAERAIEKMNGMLLNDRKVF-----VGRFKSRKEREAEL 90
Query: 88 G 88
G
Sbjct: 91 G 91
>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 = 26.2 bits (56), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 37 VGNVYIKFRREEDAEKAVNDLNNRWFGGRPV 67
G + F ++A AV DLN+R G R V
Sbjct: 57 TGEAXVAFESRDEATAAVIDLNDRPIGSRKV 87
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 26.2 bits (56), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
N +D F G+IE + D + +G ++ + DA+KA+N LN
Sbjct: 15 NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLN 67
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 26.2 bits (56), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 7 NFFEDVFVECEDKYGEIEEMNVC-DNLGDHLVGNVYIKFRREEDAEKAVNDLN 58
N +D F G+IE + D + +G ++ + DA+KA+N LN
Sbjct: 15 NMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAINTLN 67
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In
Rna-Binding Protein 14
Length = 90
Score = 26.2 bits (56), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 13/45 (28%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 29 CDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSP 73
CD + D+ ++ +E DA+ A+ LN + G+ + ELS
Sbjct: 39 CDVVKDY----AFVHMEKEADAKAAIAQLNGKEVKGKRINVELST 79
>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 = 6.2, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 18/37 (48%)
Query: 40 VYIKFRREEDAEKAVNDLNNRWFGGRPVYAELSPVTD 76
++ F EDA +A+ LN + G P+ L+ D
Sbjct: 54 AFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 90
>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 = 25.8 bits (55), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 28/63 (44%), Gaps = 4/63 (6%)
Query: 9 FEDVFVECEDKYGEIEEMNVCDNLGDHLVGNVYIKFRREEDAEKAVNDLNNRWFGGRPVY 68
+++F E +G +++ V + +G + F R+ DA KA N GRP
Sbjct: 46 IQELFAE----FGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYNGVPLDGRPXN 101
Query: 69 AEL 71
+L
Sbjct: 102 IQL 104
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
0.323 0.141 0.458
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,466,041
Number of Sequences: 62578
Number of extensions: 136911
Number of successful extensions: 318
Number of sequences better than 100.0: 50
Number of HSP's better than 100.0 without gapping: 33
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 277
Number of HSP's gapped (non-prelim): 58
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 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)