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= 030251
         (180 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: 27  RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGY 86
           R LGLD+G K +G+++SD     A  +  +   +   D        LI ++ ++  ++G+
Sbjct: 4   RILGLDLGTKTLGVALSDEXGWTAQGIETIKINEAEGDYGLSRLSELIKDYTIDKIVLGF 63

Query: 87  PFNRQQNAADAVQV-KLFIDDLSATKKLEDMKYAYWNEGFTSKGVELLLNPLDLHPVEYK 145
           P N         +  + F   L  T    ++    W+E  T+   E  L   D+   + K
Sbjct: 64  PKNXNGTVGPRGEASQTFAKVLETTY---NVPVVLWDERLTTXAAEKXLIAADVSRQKRK 120

Query: 146 TILDKFAAVGILQEYLDNAN 165
            ++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: 27  RFLGLDVGDKYVGLSISDPKNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEG---FI 83
           R   LDVG+  +GL++ +    +AS    L+RK      + ED  +L+     EG    +
Sbjct: 2   RVGALDVGEARIGLAVGEEGVPLASGRGYLVRKT-----LEEDVEALLDFVRREGLGKLV 56

Query: 84  VGYPFNRQ-QNAADAVQVKLFIDDLSATKKLEDMKYAYWNEGFTSK 128
           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 = 2.9,   Method: Compositional matrix adjust.
 Identities = 19/64 (29%), Positives = 31/64 (48%)

Query: 54  SVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFIDDLSATKKL 113
            V +R+ N   ++A   +  IS+ N++ F   Y    ++  A   + +LF  D  ATK L
Sbjct: 114 GVPIRRVNQAYVIATSTKVDISKVNVQKFDDKYFAREKKTRAKKTEGELFESDKEATKNL 173

Query: 114 EDMK 117
            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 = 28.1 bits (61), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 5/60 (8%)

Query: 46  KNKIASPLSVLLRKKNTIDLMAEDFRSLISEFNLEGFIVGYPFNRQQNAADAVQVKLFID 105
           + +  SPL++   K+  ++L      SL   +NL GF +G+    ++  A   +VK  ID
Sbjct: 206 EGEAPSPLALPGAKERVVELF-----SLSKSYNLAGFRLGFALGSEEALARLERVKGVID 260


>pdb|2GIX|A Chain A, Cytoplasmic Domain Structure Of Kir2.1 Containing
           Andersen's Mutation R218q And Rescue Mutation T309k
 pdb|2GIX|B Chain B, Cytoplasmic Domain Structure Of Kir2.1 Containing
           Andersen's Mutation R218q And Rescue Mutation T309k
 pdb|2GIX|C Chain C, Cytoplasmic Domain Structure Of Kir2.1 Containing
           Andersen's Mutation R218q And Rescue Mutation T309k
 pdb|2GIX|D Chain D, Cytoplasmic Domain Structure Of Kir2.1 Containing
           Andersen's Mutation R218q And Rescue Mutation T309k
          Length = 208

 Score = 26.6 bits (57), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 13/54 (24%), Positives = 28/54 (51%)

Query: 3   LQMKYVKPLRLFEQMLKRKVSKRGRFLGLDVGDKYVGLSISDPKNKIASPLSVL 56
           LQ  ++    +  Q+LK +++  G ++ LD  D  VG      +  + SP++++
Sbjct: 54  LQKSHLVEAHVRAQLLKSRITSEGEYIPLDQIDINVGFDSGIDRIFLVSPITIV 107


  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    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,013,406
Number of Sequences: 62578
Number of extensions: 200100
Number of successful extensions: 491
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 487
Number of HSP's gapped (non-prelim): 5
length of query: 180
length of database: 14,973,337
effective HSP length: 93
effective length of query: 87
effective length of database: 9,153,583
effective search space: 796361721
effective search space used: 796361721
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)