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= 048449
         (288 letters)

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

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



>pdb|3IZ3|B Chain B, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
 pdb|3IZ3|C Chain C, Cryoem Structure Of Cytoplasmic Polyhedrosis Virus
 pdb|3J17|B Chain B, Structure Of A Transcribing Cypovirus By Cryo-Electron
            Microscopy
 pdb|3J17|C Chain C, Structure Of A Transcribing Cypovirus By Cryo-Electron
            Microscopy
          Length = 1333

 Score = 30.0 bits (66), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 76   VPTAISHGLWLNIPDYDAPTQLVKPRERNSRYVDA--VMTIPKGSLFPMCGMN 126
            + + I     ++I D +   +++ P E  +++VDA  +MT PKG LF +  M+
Sbjct: 1156 IASVIKSNWVVDIHDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMD 1208


>pdb|3CNF|A Chain A, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus By
            Cryo-Electron Microscopy
 pdb|3CNF|B Chain B, 3.88 Angstrom Structure Of Cytoplasmic Polyhedrosis Virus By
            Cryo-Electron Microscopy
 pdb|3IZX|B Chain B, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
            Virus
 pdb|3IZX|C Chain C, 3.1 Angstrom Cryoem Structure Of Cytoplasmic Polyhedrosis
            Virus
          Length = 1333

 Score = 29.6 bits (65), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 16/53 (30%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 76   VPTAISHGLWLNIPDYDAPTQLVKPRERNSRYVDA--VMTIPKGSLFPMCGMN 126
            + + I     ++I D +   +++ P E  +++VDA  +MT PKG LF +  M+
Sbjct: 1156 IASVIKSNWVVDILDIEYTAEVMTPSEGYTQHVDAESIMTAPKGKLFHLQFMD 1208


>pdb|3NA8|A Chain A, Crystal Structure Of A Putative Dihydrodipicolinate
           Synthetase From Pseudomonas Aeruginosa
 pdb|3NA8|B Chain B, Crystal Structure Of A Putative Dihydrodipicolinate
           Synthetase From Pseudomonas Aeruginosa
 pdb|3NA8|C Chain C, Crystal Structure Of A Putative Dihydrodipicolinate
           Synthetase From Pseudomonas Aeruginosa
 pdb|3NA8|D Chain D, Crystal Structure Of A Putative Dihydrodipicolinate
           Synthetase From Pseudomonas Aeruginosa
          Length = 315

 Score = 29.3 bits (64), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 26/81 (32%), Positives = 35/81 (43%), Gaps = 10/81 (12%)

Query: 48  PLFFNTLYDPYRDG------ADFVRGYP---FSLREGVPTAISHGLWLNIPDYDAPTQLV 98
           P     LY    DG      A F R  P   F LR G+PT I  GL L+  +  AP   V
Sbjct: 235 PTLNGQLYQAVLDGDLEKARALFYRQLPLLDFILRRGLPTTIKAGLGLSGLEVGAPRLPV 294

Query: 99  KPRE-RNSRYVDAVMTIPKGS 118
           +  +    RY+  ++   +GS
Sbjct: 295 QALDTEGCRYLQGLLEELRGS 315


>pdb|2YWE|A Chain A, Crystal Structure Of Lepa From Aquifex Aeolicus
 pdb|2YWF|A Chain A, Crystal Structure Of Gmppnp-Bound Lepa From Aquifex
           Aeolicus
 pdb|2YWH|A Chain A, Crystal Structure Of Gdp-Bound Lepa From Aquifex Aeolicus
          Length = 600

 Score = 29.3 bits (64), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 45  PSTPLFFNTLYDPYRDGADFVRGYPFSLREG 75
           P   L F++ YDPYR    FVR +   ++ G
Sbjct: 192 PLKALIFDSYYDPYRGAVAFVRIFDGEVKPG 222


>pdb|2YWG|A Chain A, Crystal Structure Of Gtp-Bound Lepa From Aquifex Aeolicus
          Length = 600

 Score = 28.9 bits (63), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 12/31 (38%), Positives = 17/31 (54%)

Query: 45  PSTPLFFNTLYDPYRDGADFVRGYPFSLREG 75
           P   L F++ YDPYR    FVR +   ++ G
Sbjct: 192 PLKALIFDSYYDPYRGAVAFVRIFDGEVKPG 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
   0.320    0.138    0.435 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,180,008
Number of Sequences: 62578
Number of extensions: 404598
Number of successful extensions: 953
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 951
Number of HSP's gapped (non-prelim): 8
length of query: 288
length of database: 14,973,337
effective HSP length: 98
effective length of query: 190
effective length of database: 8,840,693
effective search space: 1679731670
effective search space used: 1679731670
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: 51 (24.3 bits)