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= 026576
         (236 letters)

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

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



>pdb|1YR6|A Chain A, Pab0955 Crystal Structure : A Gtpase In Apo Form From
           Pyrococcus Abyssi
 pdb|1YR7|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gtp-Gamma-S Bound
           Form From Pyrococcus Abyssi
 pdb|1YR8|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gtp Bound Form
           From Pyrococcus Abyssi
 pdb|1YR9|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Po4 Bound
           Form From Pyrococcus Abyssi
 pdb|1YRA|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp Bound Form
           From Pyrococcus Abyssi
 pdb|1YRA|B Chain B, Pab0955 Crystal Structure : A Gtpase In Gdp Bound Form
           From Pyrococcus Abyssi
 pdb|1YRB|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
           Form From Pyrococcus Abyssi
 pdb|1YRB|B Chain B, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
           Form From Pyrococcus Abyssi
 pdb|2OXR|A Chain A, Pab0955 Crystal Structure : A Gtpase In Gdp And Mg Bound
           Form From Pyrococcus Abyssi (After Gtp Hydrolysis)
          Length = 262

 Score = 50.4 bits (119), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 1/78 (1%)

Query: 4   VNLDPAAENFDYPVAMDIRELISLEDVMEELGLGPNGGLIYCMEHLEDNLDDWXXXXXXX 63
           VNLD   +   Y  ++D+RE +++E++M E G GPNG ++   + L +  +++       
Sbjct: 47  VNLDTGVKELPYEPSIDVREFVTVEEIMRE-GYGPNGAIVESYDRLMEKFNEYLNKILRL 105

Query: 64  XXXXXXXVFDCPGQIELF 81
                  + D PGQ+E F
Sbjct: 106 EKENDYVLIDTPGQMETF 123


>pdb|2F8M|A Chain A, Ribose 5-Phosphate Isomerase From Plasmodium Falciparum
 pdb|2F8M|B Chain B, Ribose 5-Phosphate Isomerase From Plasmodium Falciparum
          Length = 244

 Score = 29.3 bits (64), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 25/39 (64%), Gaps = 1/39 (2%)

Query: 186 VDEYSMVSFMPLDLRKESSIRYVLSQIDNCIQWGEDADL 224
           VDEY + S M + L   S++ YVL +IDN ++ G+  D+
Sbjct: 21  VDEY-VQSNMTIGLGTGSTVFYVLERIDNLLKSGKLKDV 58


>pdb|3PCO|B Chain B, Crystal Structure Of E. Coli Phenylalanine-Trna Synthetase
           Complexed With Phenylalanine And Amp
 pdb|3PCO|D Chain D, Crystal Structure Of E. Coli Phenylalanine-Trna Synthetase
           Complexed With Phenylalanine And Amp
          Length = 795

 Score = 28.1 bits (61), Expect = 4.6,   Method: Composition-based stats.
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 14  DYPVAMDIRELISLEDVMEELGLGPN 39
           D P+  DIRE + L+D   E+ + PN
Sbjct: 140 DAPIGTDIREYLKLDDNTIEISVTPN 165


>pdb|2CXX|A Chain A, Crystal Structure Of A Probable Gtp-binding Protein Engb
 pdb|2CXX|B Chain B, Crystal Structure Of A Probable Gtp-binding Protein Engb
 pdb|2CXX|C Chain C, Crystal Structure Of A Probable Gtp-binding Protein Engb
          Length = 190

 Score = 27.7 bits (60), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 13/49 (26%), Positives = 30/49 (61%)

Query: 131 QLELPHVNILSKMDLVTNKKEIEDYLNPESQFLLSELNQHMAPQFAKLN 179
           +L++P +  ++K+D + N +E+ ++L  + +  LSE+++   P  AK  
Sbjct: 120 ELDIPTIVAVNKLDKIKNVQEVINFLAEKFEVPLSEIDKVFIPISAKFG 168


>pdb|2DIY|A Chain A, The Solution Structure Of The Thioredoxin Domain Of Human
           Thioredoxin-Like Protein 2
          Length = 130

 Score = 27.7 bits (60), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 172 APQFAKLNKSLIELVDEYSMVSFMPLDLRK--ESSIRYVLSQI 212
           APQ A++N+ + EL  E   VSF+ L+     E S +Y +S +
Sbjct: 50  APQCAQMNEVMAELAKELPQVSFVKLEAEGVPEVSEKYEISSV 92


>pdb|2WZ9|A Chain A, Crystal Structure Of The Thioredoxin Domain Of Human Txnl2
          Length = 153

 Score = 27.3 bits (59), Expect = 6.9,   Method: Compositional matrix adjust.
 Identities = 16/43 (37%), Positives = 25/43 (58%), Gaps = 2/43 (4%)

Query: 172 APQFAKLNKSLIELVDEYSMVSFMPLDLRK--ESSIRYVLSQI 212
           APQ A++N+ + EL  E   VSF+ L+     E S +Y +S +
Sbjct: 44  APQCAQMNEVMAELAKELPQVSFVKLEAEGVPEVSEKYEISSV 86


  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    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,516,464
Number of Sequences: 62578
Number of extensions: 234432
Number of successful extensions: 540
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 534
Number of HSP's gapped (non-prelim): 7
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
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: 50 (23.9 bits)