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= 026590
         (236 letters)

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

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



>pdb|1NZE|A Chain A, Crystal Structure Of Psbq Polypeptide Of Photosystem Ii
           From Higher Plants
 pdb|1VYK|A Chain A, Crystal Structure Of Psbq Protein Of Photosystem Ii From
           Higher Plants
          Length = 149

 Score = 51.6 bits (122), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 32/128 (25%), Positives = 61/128 (47%)

Query: 109 NIANEKTGTRSFLKKAIYIANIGTKGRIHRLKRYAFDLLAMADLIGPDTLNYVRKYLRLK 168
           N    + GT  + K   Y+  +       R K  A ++L +   I       ++  LRL+
Sbjct: 22  NSDQARDGTLPYTKDRFYLQPLPPTEAAQRAKVSASEILNVKQFIDRKAWPSLQNDLRLR 81

Query: 169 STFMYYDFDNVISAAAPTDKQPLTDLANRLFESFEKLEVAVSTKNFPQTQSTYADTAVIL 228
           ++++ YD   VISA    +K+ L +L ++LF S + L+ A   K+  + +  Y  T   +
Sbjct: 82  ASYLRYDLKTVISAKPKDEKKSLQELTSKLFSSIDNLDHAAKIKSPTEAEKYYGQTVSNI 141

Query: 229 HEVMDRMA 236
           +EV+ ++ 
Sbjct: 142 NEVLAKLG 149


>pdb|3B8E|A Chain A, Crystal Structure Of The Sodium-Potassium Pump
 pdb|3B8E|C Chain C, Crystal Structure Of The Sodium-Potassium Pump
 pdb|3KDP|A Chain A, Crystal Structure Of The Sodium-potassium Pump
 pdb|3KDP|C Chain C, Crystal Structure Of The Sodium-potassium Pump
          Length = 998

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 18/27 (66%)

Query: 2   IISSKTATLTQNSSSMAHLANLNGVSE 28
           I S KT TLTQN  ++AH+ + N + E
Sbjct: 348 ICSDKTGTLTQNRMTVAHMWSDNQIHE 374


>pdb|3N23|A Chain A, Crystal Structure Of The High Affinity Complex Between
           Ouabain And The E2p Form Of The Sodium-Potassium Pump
 pdb|3N23|C Chain C, Crystal Structure Of The High Affinity Complex Between
           Ouabain And The E2p Form Of The Sodium-Potassium Pump
 pdb|3N2F|A Chain A, Crystal Structure Of The Sodium-Potassium Pump
 pdb|3N2F|C Chain C, Crystal Structure Of The Sodium-Potassium Pump
          Length = 992

 Score = 28.9 bits (63), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 18/27 (66%)

Query: 2   IISSKTATLTQNSSSMAHLANLNGVSE 28
           I S KT TLTQN  ++AH+ + N + E
Sbjct: 342 ICSXKTGTLTQNRMTVAHMWSDNQIHE 368


>pdb|2YWV|A Chain A, Crystal Structure Of Saicar Synthetase From Geobacillus
           Kaustophilus
 pdb|2YWV|B Chain B, Crystal Structure Of Saicar Synthetase From Geobacillus
           Kaustophilus
          Length = 244

 Score = 27.3 bits (59), Expect = 7.2,   Method: Compositional matrix adjust.
 Identities = 30/118 (25%), Positives = 48/118 (40%), Gaps = 9/118 (7%)

Query: 50  GLLGHKAENFQDQAQITRRVXXXXXXXXXXXXXXXNGVSLAEDNGLWVTGPLPVPPVYNN 109
           G+  H  E      Q+ RRV                  SLA+  GL    PL  P V   
Sbjct: 68  GIANHFIEKLSPTEQLVRRVTIIPLEVVVRNVVAG---SLAKRIGLEEGTPLEAPLVEFY 124

Query: 110 IANEKTGTRSFLKKAIYIANIGTKGRIHRLKRYAFDLLAMADLIGPDTLNYVRKYLRL 167
             N+  G    L+  I+I  + ++  +  LK+ A   LA+ D++    L++  + +RL
Sbjct: 125 YKNDDLGDPLLLEDHIFILKLASREEVAALKQAA---LAVNDVL---RLHFAERNVRL 176


  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
   0.318    0.133    0.376 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,977,162
Number of Sequences: 62578
Number of extensions: 210224
Number of successful extensions: 511
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 508
Number of HSP's gapped (non-prelim): 4
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)