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= 005524
(692 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 5/76 (6%)
Query: 383 DSTFREEDVSNYFSIYGPVQDVRI----PYQQKRMFGFVTFVYPETVKIILAKGNPHFVC 438
D + +E + +YFS YG V D I Q R FGFV F P V +LA PH +
Sbjct: 25 DWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTVLAS-RPHTLD 83
Query: 439 DARVLVKPYKEKGKVP 454
+ KP +G P
Sbjct: 84 GRNIDPKPCTPRGMQP 99
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 30/92 (32%), Positives = 46/92 (50%), Gaps = 17/92 (18%)
Query: 363 NGSAGI---VNPASRQIYLTFPADSTFREEDVSNYFSIYGPVQDVRIPYQQK----RMFG 415
+GS+G+ V S I L P +T E+D+ YFS +G V V++ K + FG
Sbjct: 3 SGSSGVKRAVQKTSDLIVLGLPWKTT--EQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFG 60
Query: 416 FVTFVYPET-VKIILAKGNPHFV----CDARV 442
FV F ET VK++ + H + CD ++
Sbjct: 61 FVRFTEYETQVKVMSQR---HMIDGRWCDCKL 89
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 36.2 bits (82), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 4/43 (9%)
Query: 385 TFREEDVSNYFSIYGPVQDVRIPY----QQKRMFGFVTFVYPE 423
T EED+ FS YGP+ ++ P ++ + F FVTF++PE
Sbjct: 19 TSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPE 61
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 388 EEDVSNYFSIYGPVQDVRIPYQQ--KRMFGFVTFVYPETV 425
E D+ FS YGP+ DV I Y Q +R GF FVY E V
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 67
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 35.0 bits (79), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 388 EEDVSNYFSIYGPVQDVRIPYQQ--KRMFGFVTFVYPETV 425
E D+ FS YGP+ 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 = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 388 EEDVSNYFSIYGPVQDVRIPYQQ--KRMFGFVTFVYPETV 425
E D+ FS YGP+ DV I Y Q +R GF FVY E V
Sbjct: 29 ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 67
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 20/40 (50%), Positives = 23/40 (57%), Gaps = 3/40 (7%)
Query: 388 EEDVSNYFSIYGPVQDVRIPYQQ--KRMFGFVTFVYPETV 425
E D+ FS YGP+ DV I Y Q +R GF FVY E V
Sbjct: 26 ERDLREVFSKYGPIADVSIVYDQQSRRSRGF-AFVYFENV 64
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 16/32 (50%), Positives = 21/32 (65%), Gaps = 1/32 (3%)
Query: 388 EEDVSNYFSIYGPVQDVRIPYQQKRMFGFVTF 419
E+++ +FS YG V DV IP + R F FVTF
Sbjct: 19 EDELREFFSQYGDVMDVFIP-KPFRAFAFVTF 49
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 4/42 (9%)
Query: 389 EDVSNYFSIYGPVQDVRIPYQQK----RMFGFVTFVYPETVK 426
EDV +YF +G V D + + + R FGFVTF + V+
Sbjct: 14 EDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVE 55
>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 = 30.4 bits (67), Expect = 3.3, Method: Composition-based stats.
Identities = 15/42 (35%), Positives = 24/42 (57%), Gaps = 4/42 (9%)
Query: 388 EEDVSNYFSIYGPVQDVRI----PYQQKRMFGFVTFVYPETV 425
E+++ YF YG V D++I + R FGF++F P +V
Sbjct: 17 EDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSV 58
>pdb|4II1|A Chain A, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|B Chain B, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|C Chain C, Crystal Structure Of The Zinc Finger Of Zgpat
pdb|4II1|D Chain D, Crystal Structure Of The Zinc Finger Of Zgpat
Length = 167
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 232 RPCLYFARGYCKNGSSCRFVHG 253
+PC +F G C+ +CRF HG
Sbjct: 77 KPCPFFLEGKCRFKENCRFSHG 98
>pdb|1H1C|A Chain A, Histidinol-Phosphate Aminotransferase (Hisc) From
Thermotoga Maritima
pdb|1H1C|B Chain B, Histidinol-Phosphate Aminotransferase (Hisc) From
Thermotoga Maritima
pdb|1H1C|C Chain C, Histidinol-Phosphate Aminotransferase (Hisc) From
Thermotoga Maritima
pdb|1H1C|D Chain D, Histidinol-Phosphate Aminotransferase (Hisc) From
Thermotoga Maritima
Length = 335
Score = 29.6 bits (65), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/72 (25%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 115 LPNPDDLIPQTTTTMNSSALPFYGNGTGSGSSDVIDEYQLQDQLSFLNESSQNLGNKNQD 174
P P+DL+ + +NS AL Y + + I Y D FL++++ ++GN +
Sbjct: 31 FPFPEDLVDEVFRRLNSDALRIYYDSPDEELIEKILSYLDTD---FLSKNNVSVGNGADE 87
Query: 175 LFYPSQMDLSSS 186
+ Y + S
Sbjct: 88 IIYVXXLXFDRS 99
>pdb|2RHK|C Chain C, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
pdb|2RHK|D Chain D, Crystal Structure Of Influenza A Ns1a Protein In Complex
With F2f3 Fragment Of Human Cellular Factor Cpsf30,
Northeast Structural Genomics Targets Or8c And Hr6309a
Length = 72
Score = 29.3 bits (64), Expect = 8.7, Method: Composition-based stats.
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 234 CLYFARGYCKNGSSCRFVH 252
C ++ RG CK G C F+H
Sbjct: 19 CKHWLRGLCKKGDQCEFLH 37
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
0.316 0.132 0.397
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,108,332
Number of Sequences: 62578
Number of extensions: 783219
Number of successful extensions: 2063
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2053
Number of HSP's gapped (non-prelim): 17
length of query: 692
length of database: 14,973,337
effective HSP length: 106
effective length of query: 586
effective length of database: 8,340,069
effective search space: 4887280434
effective search space used: 4887280434
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: 55 (25.8 bits)