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= 039864
(666 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 33.9 bits (76), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 382 TFKDEDVSNYFSIFGPVQDVRIPY----QQKRMFGFVTFVYPE 420
T +ED+ FS +GP+ ++ P ++ + F FVTF++PE
Sbjct: 19 TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 33.9 bits (76), Expect = 0.28, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 33/73 (45%), Gaps = 5/73 (6%)
Query: 380 DSTFKDEDVSNYFSIFGPVQDVRI----PYQQKRMFGFVTFVYPETVKLILARGNPHFIC 435
D + E + +YFS +G V D I Q R FGFV F P V +LA PH +
Sbjct: 25 DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLA-SRPHTLD 83
Query: 436 DSRVLVKPYKEKG 448
+ KP +G
Sbjct: 84 GRNIDPKPCTPRG 96
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 33.1 bits (74), Expect = 0.54, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 385 DEDVSNYFSIFGPVQDVRIPYQQK----RMFGFVTFVYPETVKLILAR 428
+E + YF FG V+ + +P K R F F+TF E VK I+ +
Sbjct: 13 EEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 60
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 33.1 bits (74), Expect = 0.55, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 385 DEDVSNYFSIFGPVQDVRIPYQQK----RMFGFVTFVYPETVKLILAR 428
+E + YF FG V+ + +P K R F F+TF E VK I+ +
Sbjct: 15 EEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIMEK 62
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 32.7 bits (73), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 383 FKDEDVSNYFSIFGPVQDVRIPYQQK--RMFGFVTF 416
F+D D+ F FG + DV I + ++ + FGFVTF
Sbjct: 41 FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 76
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 32.3 bits (72), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 15/36 (41%), Positives = 22/36 (61%), Gaps = 2/36 (5%)
Query: 383 FKDEDVSNYFSIFGPVQDVRIPYQQK--RMFGFVTF 416
F+D D+ F FG + DV I + ++ + FGFVTF
Sbjct: 27 FRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTF 62
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 32.3 bits (72), Expect = 0.86, Method: Composition-based stats.
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 386 EDVSNYFSIFGPVQDVRIPYQQK----RMFGFVTFVYPETVKLI 425
EDV +YF FG V D + + + R FGFVTF + V+ +
Sbjct: 14 EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKV 57
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 31.6 bits (70), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 385 DEDVSNYFSIFGPVQDVRIPYQQK----RMFGFVTFVYPETVKLILARGNPHFICDSRVL 440
+ D+ FS +GP+ DV I Y Q+ R F FV F + K R N + R+
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRIR 88
Query: 441 V 441
V
Sbjct: 89 V 89
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 385 DEDVSNYFSIFGPVQDVRIPY--QQKRMFGFVTFVYPETV 422
+ D+ FS +GP+ DV I Y Q +R GF FVY E V
Sbjct: 60 ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 98
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 385 DEDVSNYFSIFGPVQDVRIPYQQ--KRMFGFVTFVYPETV 422
+ D+ FS +GP+ DV I Y Q +R GF FVY E V
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGFA-FVYFENV 67
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 18/40 (45%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 385 DEDVSNYFSIFGPVQDVRIPYQQ--KRMFGFVTFVYPETV 422
+ D+ FS +GP+ DV I Y Q +R GF FVY E V
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 64
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 30.4 bits (67), Expect = 3.1, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 38/80 (47%), Gaps = 19/80 (23%)
Query: 380 DSTFKDEDVSNYFSIFGPVQDVRIPYQ----QKRMFGFVTFVYPETVKLILARGNPHFIC 435
D+T KD + +YFS FG V D + + R FGFV F E+V ++ +
Sbjct: 10 DTTKKD--LKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQ------- 60
Query: 436 DSRVLVKPYKEKGKIVEKRQ 455
K +K GK+++ ++
Sbjct: 61 ------KEHKLNGKVIDPKR 74
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 30.4 bits (67), Expect = 3.8, Method: Composition-based stats.
Identities = 28/88 (31%), Positives = 42/88 (47%), Gaps = 14/88 (15%)
Query: 361 GLAEKLTSANRQIYLTFPADSTFKDEDVSNYFSIFGPVQDVRIPYQQK----RMFGFVTF 416
G+ + + I L P +T ++D+ YFS FG V V++ K + FGFV F
Sbjct: 7 GVKRAVQKTSDLIVLGLPWKTT--EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF 64
Query: 417 VYPET-VKLILARGNPHFI----CDSRV 439
ET VK++ R H I CD ++
Sbjct: 65 TEYETQVKVMSQR---HMIDGRWCDCKL 89
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 0.132 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,841,043
Number of Sequences: 62578
Number of extensions: 547052
Number of successful extensions: 1116
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 1115
Number of HSP's gapped (non-prelim): 13
length of query: 666
length of database: 14,973,337
effective HSP length: 105
effective length of query: 561
effective length of database: 8,402,647
effective search space: 4713884967
effective search space used: 4713884967
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)