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= 025926
         (246 letters)

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

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



>pdb|1BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, Minimized
           Average
 pdb|2BBY|A Chain A, Dna-Binding Domain From Human Rap30, Nmr, 30 Structures
          Length = 69

 Score = 56.2 bits (134), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 25/64 (39%), Positives = 43/64 (67%)

Query: 175 RRDRGEMEDIMFKLFERQSNWTLRQLIQETDQPEQFLKDMLKDLCVYNNKGSNQGSYELK 234
           R D+  + D++F  FE+   + L+ L+  T QP  +LK++LK++ V N KG ++ ++ELK
Sbjct: 3   RADKQHVLDMLFSAFEKHQYYNLKDLVDITKQPVVYLKEILKEIGVQNVKGIHKNTWELK 62

Query: 235 PEYK 238
           PEY+
Sbjct: 63  PEYR 66


>pdb|2L5O|A Chain A, Solution Structure Of A Putative Thioredoxin From
          Neisseria Meningitidis
          Length = 153

 Score = 28.9 bits (63), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 19/42 (45%)

Query: 1  MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQS 42
           W   CP  VS   KI  + ND  +    V  V   IDP++S
Sbjct: 35 FWFPSCPGCVSEMPKIIKTANDYKNKNFQVLAVAQPIDPIES 76


>pdb|1F3U|A Chain A, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
           Human Tfiif
 pdb|1F3U|C Chain C, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
           Human Tfiif
 pdb|1F3U|E Chain E, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
           Human Tfiif
 pdb|1F3U|G Chain G, Crystal Structure Of The Rap3074 INTERACTION DOMAINS OF
           Human Tfiif
          Length = 118

 Score = 28.1 bits (61), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 19/26 (73%)

Query: 84  MSVFAESSNGKISVEGKIKNKFDMRP 109
           ++VF ESS+ K+S+EG +  + + RP
Sbjct: 92  LTVFTESSSDKLSLEGIVVQRAECRP 117


  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
   0.313    0.129    0.372 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,196,201
Number of Sequences: 62578
Number of extensions: 269199
Number of successful extensions: 406
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 403
Number of HSP's gapped (non-prelim): 4
length of query: 246
length of database: 14,973,337
effective HSP length: 96
effective length of query: 150
effective length of database: 8,965,849
effective search space: 1344877350
effective search space used: 1344877350
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 50 (23.9 bits)