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= 038639
         (229 letters)

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

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



>pdb|2JJQ|A Chain A, The Crystal Structure Of Pyrococcus Abyssi Trna
           (Uracil-54, C5)-Methyltransferase In Complex With
           S-Adenosyl-L- Homocysteine
          Length = 425

 Score = 35.4 bits (80), Expect = 0.030,   Method: Compositional matrix adjust.
 Identities = 15/70 (21%), Positives = 39/70 (55%), Gaps = 2/70 (2%)

Query: 153 IENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFL 212
           I    +G    G + K+++ID+C +  + +   +  ++++  + ++  S +++    GFL
Sbjct: 135 ITKDGIGFRERGKWWKIVDIDECPVFGKTSREAIERLKEFIEEEKI--SVWNIKKDEGFL 192

Query: 213 KHLMLRTGSF 222
           ++++LR G F
Sbjct: 193 RYMVLREGKF 202


>pdb|2VS1|A Chain A, The Crystal Structure Of Pyrococcus Abyssi Trna
           (Uracil-54, C5)-Methyltransferase In Complex With
           S-Adenosyl-L- Homocysteine
          Length = 425

 Score = 31.2 bits (69), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 14/70 (20%), Positives = 38/70 (54%), Gaps = 2/70 (2%)

Query: 153 IENYALGLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRDPQLGLSPYDVHSHSGFL 212
           I    +G    G + K+++ID+  +  + +   +  ++++  + ++  S +++    GFL
Sbjct: 135 ITKDGIGFRERGKWWKIVDIDEXPVFGKTSREAIERLKEFIEEEKI--SVWNIKKDEGFL 192

Query: 213 KHLMLRTGSF 222
           ++++LR G F
Sbjct: 193 RYMVLREGKF 202


>pdb|3VMK|A Chain A, 3-Isopropylmalate Dehydrogenase From Shewanella Benthica
           Db21 Mt-2
 pdb|3VMK|B Chain B, 3-Isopropylmalate Dehydrogenase From Shewanella Benthica
           Db21 Mt-2
          Length = 375

 Score = 28.1 bits (61), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 16/97 (16%)

Query: 99  VADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYAL 158
           +++ GF +LC R L G  + G+   ++G   E E +F   R+  KE        I   A 
Sbjct: 136 ISEKGFDILCVRELTGGIYFGKPKGRQGE-GENEEAFDTMRYSRKEI-----RRIAKIAF 189

Query: 159 GLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRD 195
              A G   KV ++DK       AN++  +V   WR+
Sbjct: 190 E-SAQGRRKKVTSVDK-------ANVLACSV--LWRE 216


>pdb|3VML|A Chain A, Chimera 3-Isopropylmalate Dehydrogenase Between Shewanella
           Oneidensis Mr-1 (O) And Shewanella Benthica Db21 Mt-2
           (M) From N-Terminal: 20% O Middle 70% M Residual 10% O
          Length = 375

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 28/97 (28%), Positives = 44/97 (45%), Gaps = 16/97 (16%)

Query: 99  VADTGFVVLCDRVLPGEKFIGRVTRKKGSYAEMEFSFGPKRWFPKESLPKRGDHIENYAL 158
           +++ GF +LC R L G  + G+   ++G   E E +F   R+  KE        I   A 
Sbjct: 136 ISEKGFDILCVRELTGGIYFGKPKGRQGE-GENEEAFDTMRYSRKEI-----RRIAKIAF 189

Query: 159 GLHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDYWRD 195
              A G   KV ++DK       AN++  +V   WR+
Sbjct: 190 E-SAQGRRKKVTSVDK-------ANVLACSV--LWRE 216


>pdb|3IZQ|1 Chain 1, Structure Of The Dom34-Hbs1-Gdpnp Complex Bound To A
           Translating Ribosome
          Length = 611

 Score = 26.9 bits (58), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 17/47 (36%), Positives = 24/47 (51%), Gaps = 2/47 (4%)

Query: 160 LHAPGFFDKVLNIDKCLLQSEPANLVLAAVQDY--WRDPQLGLSPYD 204
            H  G FD  LN D+  L +E    + A +QDY  W +  L L+ +D
Sbjct: 16  FHDEGEFDDYLNDDEYELMNEVFPTLKAQLQDYQGWDNLSLKLALFD 62


  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    0.139    0.440 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,060,933
Number of Sequences: 62578
Number of extensions: 278530
Number of successful extensions: 420
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: 418
Number of HSP's gapped (non-prelim): 8
length of query: 229
length of database: 14,973,337
effective HSP length: 95
effective length of query: 134
effective length of database: 9,028,427
effective search space: 1209809218
effective search space used: 1209809218
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: 50 (23.9 bits)