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= 029768
(188 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To
Its Substrate AsfSF2
Length = 115
Score = 82.0 bits (201), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 36/62 (58%), Positives = 49/62 (79%), Gaps = 3/62 (4%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF 83
+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++F
Sbjct: 20 VVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKF 76
Query: 84 RN 85
R+
Sbjct: 77 RS 78
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 36/62 (58%), Positives = 49/62 (79%), Gaps = 3/62 (4%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF 83
+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++F
Sbjct: 19 VVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKF 75
Query: 84 RN 85
R+
Sbjct: 76 RS 77
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 36/62 (58%), Positives = 49/62 (79%), Gaps = 3/62 (4%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF 83
+V+GLP S SWQDLKDHMR AGDVC++ V+RD TG+V++ +DM YA+RKLD ++F
Sbjct: 19 VVSGLPPSGSWQDLKDHMREAGDVCYADVYRD---GTGVVEFVRKEDMTYAVRKLDNTKF 75
Query: 84 RN 85
R+
Sbjct: 76 RS 77
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 78.6 bits (192), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 38/62 (61%), Positives = 50/62 (80%), Gaps = 3/62 (4%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGMTGIVDYTSYDDMKYAIRKLDRSEF 83
LV+GLP S SWQDLKDHMR AGDVC++ V +D GM G+V+Y +DM+YA+RKLD ++F
Sbjct: 19 LVSGLPPSGSWQDLKDHMREAGDVCYADVQKD--GM-GMVEYLRKEDMEYALRKLDDTKF 75
Query: 84 RN 85
R+
Sbjct: 76 RS 77
>pdb|2OSR|A Chain A, Nmr Structure Of Rrm-2 Of Yeast Npl3 Protein
Length = 87
Score = 38.1 bits (87), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 27 GLPSSASWQDLKDHMRRAG-DVCFSQV-FRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR 84
LP SWQDLKD R + FS V RD G TG +++ S + + A+ +L+ EFR
Sbjct: 13 NLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNNIEFR 71
>pdb|2JVR|A Chain A, Segmental Isotope Labeling Of Npl3p
Length = 111
Score = 37.7 bits (86), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 3/60 (5%)
Query: 27 GLPSSASWQDLKDHMRRAG-DVCFSQV-FRDRGGMTGIVDYTSYDDMKYAIRKLDRSEFR 84
LP SWQDLKD R + FS V RD G TG +++ S + + A+ +L+ EFR
Sbjct: 35 NLPEGCSWQDLKDLARENSLETTFSSVNTRDFDG-TGALEFPSEEILVEALERLNNIEFR 93
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 29.3 bits (64), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 18/50 (36%), Positives = 28/50 (56%), Gaps = 4/50 (8%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRD-RGGMT---GIVDYTSYD 69
+V GLP + QDLK++ G+V QV +D + G + G V +T Y+
Sbjct: 19 IVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYE 68
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 26.6 bits (57), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM--TGIVDYTSYDDMKYAIRKLD 79
V LP +W+ LKD G V ++ + + G G+V + S + + A R ++
Sbjct: 12 FVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 69
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain
In Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 26.6 bits (57), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 24 LVTGLPSSASWQDLKDHMRRAGDVCFSQVFRDRGGM--TGIVDYTSYDDMKYAIRKLD 79
V LP +W+ LKD G V ++ + + G G+V + S + + A R ++
Sbjct: 9 FVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERACRMMN 66
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
0.324 0.138 0.442
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,251,391
Number of Sequences: 62578
Number of extensions: 63333
Number of successful extensions: 132
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 123
Number of HSP's gapped (non-prelim): 10
length of query: 188
length of database: 14,973,337
effective HSP length: 93
effective length of query: 95
effective length of database: 9,153,583
effective search space: 869590385
effective search space used: 869590385
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 48 (23.1 bits)