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= 024417
         (268 letters)

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

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



>pdb|3GPI|A Chain A, Structure Of Putative Nad-Dependent EpimeraseDEHYDRATASE
           From Methylobacillus Flagellatus
          Length = 286

 Score = 35.8 bits (81), Expect = 0.026,   Method: Compositional matrix adjust.
 Identities = 21/72 (29%), Positives = 34/72 (47%), Gaps = 2/72 (2%)

Query: 164 LAALSWNGEGSFLFTSSSAIYDCSDNGACDEDSPVVPIGRSPRTDVLLKAEKVILEFGGC 223
           L+AL         F SS+ +Y        DED+P  PI +      +L+AE ++  +   
Sbjct: 93  LSALEGAPLQHVFFVSSTGVYGQEVEEWLDEDTP--PIAKDFSGKRMLEAEALLAAYSST 150

Query: 224 VLRLAGLYKADR 235
           +LR +G+Y   R
Sbjct: 151 ILRFSGIYGPGR 162


>pdb|1VLV|A Chain A, Crystal Structure Of Ornithine Carbamoyltransferase
           (tm1097) From Thermotoga Maritima At 2.25 A Resolution
          Length = 325

 Score = 28.5 bits (62), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 4/71 (5%)

Query: 200 PIGRSPRTDVLLKAEKVILEFGGCVLRLAGLYKADRGAHV----YWLQKGTVDSRPDHIL 255
           P    PR+DV  + ++++ E  G V   + L +A  GA V     W   G  D   + + 
Sbjct: 200 PEELKPRSDVFKRCQEIVKETDGSVSFTSNLEEALAGADVVYTDVWASMGEEDKEKERMA 259

Query: 256 NLIHYELPSRL 266
            L  Y++  R+
Sbjct: 260 LLKPYQVNERV 270


  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
   0.319    0.135    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,183,684
Number of Sequences: 62578
Number of extensions: 334926
Number of successful extensions: 655
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 655
Number of HSP's gapped (non-prelim): 3
length of query: 268
length of database: 14,973,337
effective HSP length: 97
effective length of query: 171
effective length of database: 8,903,271
effective search space: 1522459341
effective search space used: 1522459341
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)