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= 024601
         (265 letters)

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

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



>pdb|1JMT|A Chain A, X-Ray Structure Of A Core U2af65U2AF35 HETERODIMER
          Length = 104

 Score = 56.2 bits (134), Expect = 2e-08,   Method: Compositional matrix adjust.
 Identities = 25/55 (45%), Positives = 36/55 (65%), Gaps = 7/55 (12%)

Query: 41  KYGEIESLNICDNLADHM-------FREEEQAARALKSLSGRFYAGRPIIVDFSP 88
           KYGE+E +N+CDNL DH+       FR EE A +A+  L+ R++ G+PI  + SP
Sbjct: 50  KYGEVEEMNVCDNLGDHLVGNVYVKFRREEDAEKAVIDLNNRWFNGQPIHAELSP 104


>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat
          Specific Factor 1 Variant
          Length = 112

 Score = 32.3 bits (72), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 4/47 (8%)

Query: 40 NKYGEIESLNICD----NLADHMFREEEQAARALKSLSGRFYAGRPI 82
          +K+G+I  L + D     +A   FR+ E+A   +++L GR++ GR I
Sbjct: 48 SKFGQIRKLLLFDRHPDGVASVSFRDPEEADYCIQTLDGRWFGGRQI 94


>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
          Apobec-1 Complementation Factor, Acf
          Length = 99

 Score = 27.3 bits (59), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 24/51 (47%)

Query: 41 KYGEIESLNICDNLADHMFREEEQAARALKSLSGRFYAGRPIIVDFSPVTD 91
          K G +E +    + A   F   E A  A+K+L+G+   G PI V  +   D
Sbjct: 40 KPGAVERVKKIRDYAFVHFSNREDAVEAMKALNGKVLDGSPIEVTLAKPVD 90


  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    0.135    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,492,808
Number of Sequences: 62578
Number of extensions: 134041
Number of successful extensions: 324
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 319
Number of HSP's gapped (non-prelim): 5
length of query: 265
length of database: 14,973,337
effective HSP length: 97
effective length of query: 168
effective length of database: 8,903,271
effective search space: 1495749528
effective search space used: 1495749528
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: 50 (23.9 bits)