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= 045845
(69 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 38.9 bits (89), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 33 FGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
+ F+ ++R EDA AIR LD TE+ G+ +HV+ S S
Sbjct: 46 YAFVHMERAEDAVEAIRGLDNTEFQGKRMHVQLSTS 81
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 33.9 bits (76), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 16/37 (43%), Positives = 22/37 (59%)
Query: 32 GFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
GF F+ + EDA AAI ++E+E GR I V +K
Sbjct: 55 GFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAKP 91
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 33.5 bits (75), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 31 HGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
G+GF+ +EDAD AI+ +D + G+ I V K+ +
Sbjct: 57 QGYGFVEFLSEEDADYAIKIMDMIKLYGKPIRVNKASA 94
>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 = 33.5 bits (75), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 32 GFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSK 67
GF F+ + EDA AAI ++E+E GR I V +K
Sbjct: 50 GFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 33.5 bits (75), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/36 (44%), Positives = 22/36 (61%)
Query: 32 GFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSK 67
GF F+ + EDA AAI ++E+E GR I V +K
Sbjct: 48 GFAFVEFELAEDAAAAIDNMNESELFGRTIRVNLAK 83
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 32.3 bits (72), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 32 GFGFLSLDRDEDADAAIRTLDETEWNGRIIHV 63
GF F+ + EDA AAI ++E+E GR I V
Sbjct: 106 GFAFVEFELAEDAAAAIDNMNESELFGRTIRV 137
>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 = 32.0 bits (71), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 20/32 (62%)
Query: 32 GFGFLSLDRDEDADAAIRTLDETEWNGRIIHV 63
GF F+ + EDA AAI ++E+E GR I V
Sbjct: 45 GFAFVEFELAEDAAAAIDNMNESELFGRTIRV 76
>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 = 0.27, Method: Compositional matrix adjust.
Identities = 14/32 (43%), Positives = 18/32 (56%), Gaps = 5/32 (15%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRII 61
S GFGF+ E+A A+ TE NGRI+
Sbjct: 54 SKGFGFVCFSSPEEATKAV-----TEMNGRIV 80
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 28 RDSHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
R S GFGF++ + DAD A L T GR I V + +
Sbjct: 52 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 92
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 29.6 bits (65), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 28 RDSHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
R S GFGF++ + DAD A L T GR I V + +
Sbjct: 66 RGSKGFGFVTFENSADADRAREKLHGTVVEGRKIEVNNATA 106
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 29.3 bits (64), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 13/39 (33%), Positives = 22/39 (56%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
G+GF E A +A+R L+ E++GR + V+ + S
Sbjct: 49 PKGYGFCEYQDQETALSAMRNLNGREFSGRALRVDNAAS 87
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 28.9 bits (63), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 24/38 (63%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSK 67
S GFGF+ + +EDA AA +++ E +G + ++ +K
Sbjct: 53 SKGFGFVDFNSEEDAKAAKEAMEDGEIDGNKVTLDWAK 90
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 28.9 bits (63), Expect = 0.76, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKST 69
S G+GF++ DAD AI TL+ + + I V ++ +
Sbjct: 45 SLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 28.9 bits (63), Expect = 0.82, Method: Compositional matrix adjust.
Identities = 13/40 (32%), Positives = 22/40 (55%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKST 69
S G+GF++ DAD AI TL+ + + I V ++ +
Sbjct: 45 SLGYGFVNYSDPNDADKAINTLNGLKLQTKTIKVSYARPS 84
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.5 bits (62), Expect = 0.88, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 20/38 (52%)
Query: 27 NRDSHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVE 64
N S G+ F+ EDA A+ + ++ E GR I +E
Sbjct: 49 NGKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLE 86
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 28.1 bits (61), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 12/37 (32%), Positives = 23/37 (62%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKS 66
S GFGF++ + +DA A+ ++ +GR I V+++
Sbjct: 53 SRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVDQA 89
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKST 69
S GF F+S R EDA AI + ++ I++VE +K +
Sbjct: 56 SKGFAFISFHRREDAARAIAGVSGFGYDHLILNVEWAKPS 95
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor
9g8
Length = 101
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 28 RDSHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKS 66
R+ GF F+ + DA+ A+R LD G + VE S
Sbjct: 34 RNPPGFAFVEFEDPRDAEDAVRGLDGKVICGSRVRVELS 72
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 26.9 bits (58), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHV 63
S G+GF+S +DA A+ ++ + NGR + +
Sbjct: 128 SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 161
>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
Length = 104
Score = 26.9 bits (58), Expect = 3.0, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 32 GFGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSK 67
G ++ R+EDA+ A+ L+ +NG+ IH E S
Sbjct: 69 GNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 26.6 bits (57), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 11/34 (32%), Positives = 20/34 (58%)
Query: 30 SHGFGFLSLDRDEDADAAIRTLDETEWNGRIIHV 63
S G+GF+S +DA A+ ++ + NGR + +
Sbjct: 42 SRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLRI 75
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 33 FGFLSLDRDEDADAAIRTLDETEWNGRIIHVEKSKS 68
+GF+ ++ A+ AIR L + +G I+VE SK+
Sbjct: 44 YGFVHIEDKTAAEDAIRNLHHYKLHGVNINVEASKN 79
>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 = 25.4 bits (54), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 30 SHGFGFLSLDRDEDADAAIRT 50
S GFGFLS ++ D ++T
Sbjct: 44 SRGFGFLSFEKPSSVDEVVKT 64
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.312 0.129 0.367
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,648,697
Number of Sequences: 62578
Number of extensions: 42272
Number of successful extensions: 96
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 69
Number of HSP's gapped (non-prelim): 28
length of query: 69
length of database: 14,973,337
effective HSP length: 39
effective length of query: 30
effective length of database: 12,532,795
effective search space: 375983850
effective search space used: 375983850
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 45 (21.9 bits)