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= 030509
         (176 letters)

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

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



>pdb|1VHX|A Chain A, Crystal Structure Of Putative Holliday Junction Resolvase
 pdb|1VHX|B Chain B, Crystal Structure Of Putative Holliday Junction Resolvase
          Length = 150

 Score = 56.6 bits (135), Expect = 8e-09,   Method: Compositional matrix adjust.
 Identities = 39/140 (27%), Positives = 65/140 (46%), Gaps = 4/140 (2%)

Query: 23  RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGY 82
           R LGLD+G K +G+++SD     A  +  +   +   D        LI ++ ++  ++G+
Sbjct: 4   RILGLDLGTKTLGVALSDEXGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGF 63

Query: 83  PFNRQQNAADAVQV-KLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYK 141
           P N         +  + F   L  T    ++    W+E  T+   E  L   D+   + K
Sbjct: 64  PKNXNGTVGPRGEASQTFAKVLETTY---NVPVVLWDERLTTXAAEKXLIAADVSRQKRK 120

Query: 142 TILDKFAAVGILQEYLDNAN 161
            ++DK AAV ILQ YLD+ N
Sbjct: 121 KVIDKXAAVXILQGYLDSLN 140


>pdb|1IV0|A Chain A, Solution Structure Of The Yqgf-Family Protein (N-Terminal
           Fragment)
          Length = 98

 Score = 38.5 bits (88), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 30/106 (28%), Positives = 50/106 (47%), Gaps = 13/106 (12%)

Query: 23  RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEG---FI 79
           R   LDVG+  +GL++ +    +AS    L+RK      + ED  +L+     EG    +
Sbjct: 2   RVGALDVGEARIGLAVGEEGVPLASGRGYLVRKT-----LEEDVEALLDFVRREGLGKLV 56

Query: 80  VGYPFNRQ-QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 124
           VG P     + +A A +V   ++ L A      ++   W+E FT+K
Sbjct: 57  VGLPLRTDLKESAQAGKVLPLVEALRA----RGVEVELWDERFTTK 98


>pdb|3IZR|G Chain G, Localization Of The Large Subunit Ribosomal Proteins Into
           A 5.5 A Cryo-Em Map Of Triticum Aestivum Translating 80s
           Ribosome
          Length = 219

 Score = 28.1 bits (61), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 31/64 (48%)

Query: 50  SVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKL 109
            V +R+ N   ++A   +  IS+ N++ F   Y    ++  A   + +LF  D  ATK L
Sbjct: 114 GVPIRRVNQAYVIATSTKVDISKVNVQKFDDKYFAREKKTRAKKTEGELFESDKEATKNL 173

Query: 110 EDMK 113
            D K
Sbjct: 174 PDFK 177


>pdb|2DOU|A Chain A, Probable N-Succinyldiaminopimelate Aminotransferase
           (Ttha0342) From Thermus Thermophilus Hb8
 pdb|2DOU|B Chain B, Probable N-Succinyldiaminopimelate Aminotransferase
           (Ttha0342) From Thermus Thermophilus Hb8
          Length = 376

 Score = 27.7 bits (60), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 42  KNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 101
           + +  SPL++   K+  ++L      SL   +NL GF +G+    ++  A   +VK  ID
Sbjct: 206 EGEAPSPLALPGAKERVVELF-----SLSKSYNLAGFRLGFALGSEEALARLERVKGVID 260


  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    0.139    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,956,279
Number of Sequences: 62578
Number of extensions: 196861
Number of successful extensions: 484
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 481
Number of HSP's gapped (non-prelim): 4
length of query: 176
length of database: 14,973,337
effective HSP length: 92
effective length of query: 84
effective length of database: 9,216,161
effective search space: 774157524
effective search space used: 774157524
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: 48 (23.1 bits)