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= 027121
         (228 letters)

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

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



>pdb|3CRV|A Chain A, "xpd_helicase"
 pdb|3CRW|1 Chain 1, "xpd_apo"
          Length = 551

 Score = 30.0 bits (66), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 14/31 (45%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 166 YFSFLNLLYLGFICILTVPFLY-DRYDEHVD 195
           Y+S LN LY   +  LT P+ + DRY E +D
Sbjct: 139 YYSLLNSLYKADVIALTYPYFFIDRYREFID 169


>pdb|2G7U|A Chain A, 2.3 A Structure Of Putative Catechol Degradative Operon
           Regulator From Rhodococcus Sp. Rha1
 pdb|2G7U|B Chain B, 2.3 A Structure Of Putative Catechol Degradative Operon
           Regulator From Rhodococcus Sp. Rha1
 pdb|2G7U|C Chain C, 2.3 A Structure Of Putative Catechol Degradative Operon
           Regulator From Rhodococcus Sp. Rha1
 pdb|2G7U|D Chain D, 2.3 A Structure Of Putative Catechol Degradative Operon
           Regulator From Rhodococcus Sp. Rha1
          Length = 257

 Score = 27.7 bits (60), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 10/40 (25%), Positives = 22/40 (55%)

Query: 84  HISITSMLALFIWSKGAEFFNWKPPQIPEVILRESTFREV 123
           ++S+ + +  +  S G     W P  + E ++ ESTF+++
Sbjct: 129 NVSVGTRVPAYATSXGRALLAWAPADVVERVVAESTFQKL 168


  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
   0.327    0.144    0.440 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,719,730
Number of Sequences: 62578
Number of extensions: 205922
Number of successful extensions: 446
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 445
Number of HSP's gapped (non-prelim): 2
length of query: 228
length of database: 14,973,337
effective HSP length: 95
effective length of query: 133
effective length of database: 9,028,427
effective search space: 1200780791
effective search space used: 1200780791
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)