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= 002970
         (862 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3EF1|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
           Phosphatase
          Length = 442

 Score = 43.5 bits (101), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 11/76 (14%)

Query: 186 FEVYVCTMAERDYALEMWRLLDPESNLINTKELLDRIVCVK-SGS--RKSLFNVFQDGTC 242
           +E+++ TM  + YA E+ +++DP   L       DR++    SGS  +KSL  +F    C
Sbjct: 99  YELHIYTMGTKAYAKEVAKIIDPTGKLFQ-----DRVLSRDDSGSLAQKSLRRLF---PC 150

Query: 243 HPKMALVIDDRLKVWD 258
              M +VIDDR  VWD
Sbjct: 151 DTSMVVVIDDRGDVWD 166


>pdb|3EF0|A Chain A, The Structure Of Fcp1, An Essential Rna Polymerase Ii Ctd
           Phosphatase
          Length = 372

 Score = 43.1 bits (100), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 28/76 (36%), Positives = 42/76 (55%), Gaps = 11/76 (14%)

Query: 186 FEVYVCTMAERDYALEMWRLLDPESNLINTKELLDRIVCVK-SGS--RKSLFNVFQDGTC 242
           +E+++ TM  + YA E+ +++DP   L       DR++    SGS  +KSL  +F    C
Sbjct: 91  YELHIYTMGTKAYAKEVAKIIDPTGKLFQ-----DRVLSRDDSGSLAQKSLRRLF---PC 142

Query: 243 HPKMALVIDDRLKVWD 258
              M +VIDDR  VWD
Sbjct: 143 DTSMVVVIDDRGDVWD 158


>pdb|2L3C|A Chain A, Solution Structure Of Adar2 Dsrbm1 Bound To Lsl Rna
          Length = 74

 Score = 33.9 bits (76), Expect = 0.35,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 26/39 (66%), Gaps = 5/39 (12%)

Query: 781 VEIDGQVLGKGIGSTWDEAKMQAAEKALGSLRSMFGQFP 819
           VE++GQV  +G G T  +AK+ AAEKAL S    F QFP
Sbjct: 40  VEVNGQVF-EGSGPTKKKAKLHAAEKALRS----FVQFP 73


>pdb|2B7T|A Chain A, Structure Of Adar2 Dsrbm1
          Length = 73

 Score = 33.9 bits (76), Expect = 0.41,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 26/39 (66%), Gaps = 5/39 (12%)

Query: 781 VEIDGQVLGKGIGSTWDEAKMQAAEKALGSLRSMFGQFP 819
           VE++GQV  +G G T  +AK+ AAEKAL S    F QFP
Sbjct: 40  VEVNGQVF-EGSGPTKKKAKLHAAEKALRS----FVQFP 73


>pdb|2L3J|A Chain A, The Solution Structure Of The Adar2 Dsrbm-Rna Complex
           Reveals A Sequence-Specific Read Out Of The Minor Groove
          Length = 236

 Score = 33.9 bits (76), Expect = 0.45,   Method: Compositional matrix adjust.
 Identities = 24/52 (46%), Positives = 31/52 (59%), Gaps = 8/52 (15%)

Query: 781 VEIDGQVLGKGIGSTWDEAKMQAAEKALGSLRSMFGQFP---QKHQGSPRSL 829
           VE++GQV  +G G T  +AK+ AAEKAL S    F QFP   + H    R+L
Sbjct: 40  VEVNGQVF-EGSGPTKKKAKLHAAEKALRS----FVQFPNASEAHLAMGRTL 86


>pdb|3V7I|A Chain A, Germicidin Synthase (Gcs) From Streptomyces Coelicolor, A
           Type Iii Polyketide Synthase
          Length = 413

 Score = 29.3 bits (64), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 21/94 (22%), Positives = 41/94 (43%), Gaps = 4/94 (4%)

Query: 108 AENDQVNENGKVIKVQSEVVPA----LSDSHQALVRPLIRLQEKNIILTRINPQIRDTSV 163
           A +  +   G ++ +++ V P     L  + +ALVR     Q+ N  +  +       +V
Sbjct: 67  AASTGIESRGWMLPLEAAVAPGGGGDLGAAREALVRDGFTEQDANRAIAALKAVPASQTV 126

Query: 164 LVRLRPAWEDLRSYLTARGRKRFEVYVCTMAERD 197
             R  PAWE +++Y     R   ++    +A+ D
Sbjct: 127 QERTAPAWEAVQAYGERAARGALQIAGLDVADVD 160


  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    0.134    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 23,980,614
Number of Sequences: 62578
Number of extensions: 964804
Number of successful extensions: 2051
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 2049
Number of HSP's gapped (non-prelim): 10
length of query: 862
length of database: 14,973,337
effective HSP length: 107
effective length of query: 755
effective length of database: 8,277,491
effective search space: 6249505705
effective search space used: 6249505705
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: 56 (26.2 bits)