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= 033517
         (117 letters)

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

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



>pdb|2WSC|1 Chain 1, Improved Model Of Plant Photosystem I
 pdb|2WSE|1 Chain 1, Improved Model Of Plant Photosystem I
 pdb|2WSF|1 Chain 1, Improved Model Of Plant Photosystem I
          Length = 241

 Score = 32.0 bits (71), Expect = 0.080,   Method: Compositional matrix adjust.
 Identities = 17/49 (34%), Positives = 20/49 (40%), Gaps = 1/49 (2%)

Query: 60  LIAKWKKPGYERLCCLRCMQPRDHNFQTTCVCRVPKNLREEKVIECVHC 108
           + A W  PG  R   L    P D  F    +  VP NL   K  E +HC
Sbjct: 44  MAAHWM-PGEPRPAYLDGSAPGDFGFDPLGLGEVPANLERYKESELIHC 91


>pdb|2O01|1 Chain 1, The Structure Of A Plant Photosystem I Supercomplex At 3.4
           Angstrom Resolution
          Length = 187

 Score = 32.0 bits (71), Expect = 0.088,   Method: Compositional matrix adjust.
 Identities = 15/42 (35%), Positives = 17/42 (40%)

Query: 67  PGYERLCCLRCMQPRDHNFQTTCVCRVPKNLREEKVIECVHC 108
           PG  R   L    P D  F    +  VP NL   K  E +HC
Sbjct: 2   PGEPRPAYLDGSAPGDFGFDPLGLGEVPANLERYKESELIHC 43


>pdb|2DVY|A Chain A, Crystal Structure Of Restriction Endonucleases Pabi
 pdb|2DVY|B Chain B, Crystal Structure Of Restriction Endonucleases Pabi
 pdb|2DVY|C Chain C, Crystal Structure Of Restriction Endonucleases Pabi
 pdb|2DVY|D Chain D, Crystal Structure Of Restriction Endonucleases Pabi
 pdb|2DVY|E Chain E, Crystal Structure Of Restriction Endonucleases Pabi
 pdb|2DVY|F Chain F, Crystal Structure Of Restriction Endonucleases Pabi
          Length = 226

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 3/77 (3%)

Query: 18  LWPIFKIAHQKSRYIFDLYYRRKEISKELYEFCLDQGYADCNLIAKWKKPGYERLCCLRC 77
           ++ + K A     Y+ D   RR+  ++ELY F +   Y D   +AK + P  E +  +  
Sbjct: 96  IYELLKFADDVKSYLEDKGIRRESTNEELYGFNI---YEDVYPVAKKELPSGEFIGIVLK 152

Query: 78  MQPRDHNFQTTCVCRVP 94
            + R   +Q+     +P
Sbjct: 153 HKQRAVGYQSMVYVCIP 169


>pdb|3TSN|A Chain A, 4-Hydroxythreonine-4-Phosphate Dehydrogenase From
          Campylobacter Jejuni
 pdb|3TSN|B Chain B, 4-Hydroxythreonine-4-Phosphate Dehydrogenase From
          Campylobacter Jejuni
 pdb|3TSN|C Chain C, 4-Hydroxythreonine-4-Phosphate Dehydrogenase From
          Campylobacter Jejuni
 pdb|3TSN|D Chain D, 4-Hydroxythreonine-4-Phosphate Dehydrogenase From
          Campylobacter Jejuni
          Length = 367

 Score = 25.4 bits (54), Expect = 7.3,   Method: Composition-based stats.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 23 KIAHQKSRYIFDLYYRRKEISKELYEFCLDQGY 55
          KI   K    ++  + +KE S E+Y FCL  G+
Sbjct: 59 KIVAFKDDKDYEFNFIKKENSLEIYSFCLPLGF 91


  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
   0.327    0.142    0.494 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,930,065
Number of Sequences: 62578
Number of extensions: 147685
Number of successful extensions: 389
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: 384
Number of HSP's gapped (non-prelim): 7
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 45 (21.9 bits)