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= 013245
         (447 letters)

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

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



>pdb|3SQZ|A Chain A, Crystal Structure Of Hmg_coa Synthase Complexed With Coa
          Length = 389

 Score = 28.1 bits (61), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 43/185 (23%), Positives = 67/185 (36%), Gaps = 34/185 (18%)

Query: 86  NETHISSNQEKCDL--FTGEWIPDPS--GPIYSNVTCHAIEGHQNCMRNGRPDSGYLY-- 139
           NE   + ++EK D+     E   D S  G +Y     H++ G Q   R+        Y  
Sbjct: 60  NEILTAEDKEKIDMVILATESSVDQSKAGAVY----VHSLLGIQPFARSFEMKEAXCYSA 115

Query: 140 -WRWNPRDCELPRFNPERFLNFMRNKWWAFIGDSISRNHVQSLLCILSQVEQAVEVYHDE 198
               N     + +    R L    +     IG           + +L + +  + + HDE
Sbjct: 116 TAALNYAKLHVEKHPDTRVLVLASDIAKYGIGTPGESTQGAGSIAMLVKKDPRILILHDE 175

Query: 199 EYRSKR-----WQFPSYNFTLSVVWTPFLLKAEVFEDINGVSSSEIRLYLDELDTKWTEQ 253
                R     W+ P+Y        TP+         +NG+ S+  + YLD L T W E 
Sbjct: 176 TLAQTRDIMDFWR-PNYT------TTPY---------VNGMYST--KQYLDMLKTTWAEY 217

Query: 254 YKNFD 258
            K FD
Sbjct: 218 QKRFD 222


  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
   0.321    0.138    0.449 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,919,212
Number of Sequences: 62578
Number of extensions: 576951
Number of successful extensions: 970
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 968
Number of HSP's gapped (non-prelim): 4
length of query: 447
length of database: 14,973,337
effective HSP length: 102
effective length of query: 345
effective length of database: 8,590,381
effective search space: 2963681445
effective search space used: 2963681445
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (25.0 bits)