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= 041931
         (491 letters)

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

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



>pdb|3QO5|A Chain A, Crystal Structure Of The Seryl-Trna Synthetase From
           Candida Albicans
          Length = 485

 Score = 31.2 bits (69), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 11/59 (18%)

Query: 42  NVYIVTMIGFKSKINPEVVKANLEHSLLKHRRFSSLQVVDEKIEGGLKWVPTKVNLDDH 100
           N ++V   G     +PE++KA+      + +R  S+++VDE I    +WV  + +LD+H
Sbjct: 5   NAFLVEKGG-----DPEIIKAS------QKKRGDSVELVDEIIAEYKEWVKLRFDLDEH 52


>pdb|3QNE|A Chain A, Candida Albicans Seryl-Trna Synthetase
 pdb|3QO7|A Chain A, Crystal Structure Of The Seryl-Trna Synthetase From
           Candida Albicans
 pdb|3QO8|A Chain A, Crystal Structure Of Seryl-Trna Synthetase From Candida
           Albicans
          Length = 485

 Score = 31.2 bits (69), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 33/59 (55%), Gaps = 11/59 (18%)

Query: 42  NVYIVTMIGFKSKINPEVVKANLEHSLLKHRRFSSLQVVDEKIEGGLKWVPTKVNLDDH 100
           N ++V   G     +PE++KA+      + +R  S+++VDE I    +WV  + +LD+H
Sbjct: 5   NAFLVEKGG-----DPEIIKAS------QKKRGDSVELVDEIIAEYKEWVKLRFDLDEH 52


>pdb|3NDA|A Chain A, Crystal Structure Of Serpin From Tick Ixodes Ricinus
 pdb|3NDA|B Chain B, Crystal Structure Of Serpin From Tick Ixodes Ricinus
          Length = 377

 Score = 29.6 bits (65), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 52/227 (22%), Positives = 102/227 (44%), Gaps = 36/227 (15%)

Query: 32  MARMFHEP---ESNVYIVTMIGFKSKINPEVVKANLE-------------------HSLL 69
           + ++F+EP   ++ + ++  I FK + N   VK + E                    + +
Sbjct: 150 IEKLFNEPLDPDTLLVLLNAIYFKGEWNTAFVKEHTEKRQFFNGGVTPVEVDTMRLEARI 209

Query: 70  KHRRFSSLQV-VDEKIEGGLKWVPTKVNLDDHVIVPNLEPKLIDSPDKFVEDYTSSLSQT 128
           K+R F  LQV V E    GL +    +   ++  V  L+  L  + D+F ++Y S L + 
Sbjct: 210 KYRFFDDLQVEVVELPYRGLDYTMAILLPKENTGVEGLKQNL--TIDRF-QNYLSDLRER 266

Query: 129 GIKMSMPMWDLHLLNIKTSDAESVAVLRVHHSLGD--GTSLMSLLLACC--RKVSDPNEV 184
            I + +P + L       +  +S+ + ++  S  D  G +  SL ++    + V + NE 
Sbjct: 267 KITVLLPKFKLETKYSLKAPLQSLGIKQIFESGADLSGINDGSLRVSAVEHKAVVEVNEE 326

Query: 185 PTIPSVTKKIDSNGHSKGFWPYLLFKL---WLFW--NTLVDVVMFIA 226
            T+ + T  +    +S G  P ++F++   +LF+  NT  D + F+ 
Sbjct: 327 GTVAAATTGVVIVPYSLGPEP-VVFRVDHPFLFFIRNTRTDDIFFVG 372


>pdb|3SKX|A Chain A, Crystal Structure Of The Atp Binding Domain Of
           Archaeoglobus Fulgidus Copb
          Length = 280

 Score = 28.5 bits (62), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 25/124 (20%), Positives = 53/124 (42%), Gaps = 21/124 (16%)

Query: 89  KWVPTKVNLDDHV--IVPNLEPKLIDSPDKFVEDYTSSLSQTGIKMSMPMWDLHLLNIKT 146
           KWV  ++ LDD+   ++P+ + + +    +  + Y +++   G+                
Sbjct: 175 KWVAEELGLDDYFAEVLPHEKAEKVK---EVQQKYVTAMVGDGV---------------- 215

Query: 147 SDAESVAVLRVHHSLGDGTSLMSLLLACCRKVSDPNEVPTIPSVTKKIDSNGHSKGFWPY 206
           +DA ++A   V  ++G GT +           +DP +V  I  +++K  S  H    W +
Sbjct: 216 NDAPALAQADVGIAIGAGTDVAVETADIVLVRNDPRDVAAIVELSRKTYSKFHGLSAWSH 275

Query: 207 LLFK 210
             F+
Sbjct: 276 PQFE 279


  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    0.136    0.407 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,308,048
Number of Sequences: 62578
Number of extensions: 505516
Number of successful extensions: 1037
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1037
Number of HSP's gapped (non-prelim): 4
length of query: 491
length of database: 14,973,337
effective HSP length: 103
effective length of query: 388
effective length of database: 8,527,803
effective search space: 3308787564
effective search space used: 3308787564
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: 53 (25.0 bits)