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= 010974
         (496 letters)

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

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



>pdb|1IKN|D Chain D, IkappabalphaNF-Kappab Complex
          Length = 236

 Score = 29.3 bits (64), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 340 FGNNIQMTPASLSALNSPSDTTEMILQSGCE 370
           F NN+Q TP  L+ + +  +  E +L +GC+
Sbjct: 40  FQNNLQQTPLHLAVITNQPEIAEALLGAGCD 70


>pdb|1NFI|E Chain E, I-Kappa-B-AlphaNF-Kappa-B Complex
 pdb|1NFI|F Chain F, I-Kappa-B-AlphaNF-Kappa-B Complex
          Length = 213

 Score = 28.9 bits (63), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 11/31 (35%), Positives = 19/31 (61%)

Query: 340 FGNNIQMTPASLSALNSPSDTTEMILQSGCE 370
           F NN+Q TP  L+ + +  +  E +L +GC+
Sbjct: 37  FQNNLQQTPLHLAVITNQPEIAEALLGAGCD 67


>pdb|2DU7|A Chain A, Crystal Structure Of Methanococcus Jannacshii
           O-Phosphoseryl-Trna Synthetase
 pdb|2DU7|B Chain B, Crystal Structure Of Methanococcus Jannacshii
           O-Phosphoseryl-Trna Synthetase
 pdb|2DU7|C Chain C, Crystal Structure Of Methanococcus Jannacshii
           O-Phosphoseryl-Trna Synthetase
 pdb|2DU7|D Chain D, Crystal Structure Of Methanococcus Jannacshii
           O-Phosphoseryl-Trna Synthetase
          Length = 549

 Score = 28.9 bits (63), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 33/131 (25%), Positives = 59/131 (45%), Gaps = 25/131 (19%)

Query: 88  EAEDIVKDLRADLREAQDELERATYN--EKQLLDEQNSTGDVATVMTPSLENRLNTSEAA 145
           E  +I+K+L  D+ E + E  R   +  +K  +D  +   ++A  +  S E  L   E A
Sbjct: 120 EKVEIIKNLGIDIDEEKKERLREVLHLYKKGAIDGDDLVFEIAKALNVSNEMGLKVLETA 179

Query: 146 MPCLPDVQPDSVMASDVGNSTLNGTYENKMCYSENGSHKDNCYFCNSSFASIVMRRKEP- 204
            P   D++P+S        +TL              SH  + +F   + +S++ +RK P 
Sbjct: 180 FPEFKDLKPES--------TTLTLR-----------SHMTSGWFI--TLSSLIKKRKLPL 218

Query: 205 KLYR-NGCTQR 214
           KL+  + C +R
Sbjct: 219 KLFSIDRCFRR 229


>pdb|3K8W|A Chain A, Crysatl Structure Of A Bacterial Cell-Surface Flagellin
           N20c45
          Length = 326

 Score = 28.5 bits (62), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 44/201 (21%), Positives = 84/201 (41%), Gaps = 54/201 (26%)

Query: 9   ALKKAYADIILNTAKEAAARIMVSERKTIRYQQELFAAKEDALRMLLRLKQMLDAKVNEA 68
           +L++  + + +N+AK+ AA + +S+                  RM  ++K +  A+ N  
Sbjct: 8   SLQRLSSGLRINSAKDDAAGLAISD------------------RMTAQIKGLTQAQRNAN 49

Query: 69  QVVSLCQQ------------RKIDELEAQLGEAEDIVKD---LRADLREAQDELERA--- 110
             +SL Q             ++I EL  Q     +   D   L+A++ + Q E++R    
Sbjct: 50  DGISLAQTAEGALGEISNNLQRIRELAVQASNGTNTQTDRDALQAEVTQLQSEIQRVAEQ 109

Query: 111 -TYNEKQLLD------------EQNSTGDVATVM---TPSLENRLNTSEAAMPCLPDVQP 154
            ++N ++LLD                T  V+ +M   T SL   L  + + +      + 
Sbjct: 110 TSFNGQKLLDGSFNGVQFQIGANAGETIGVSKIMNAQTASLGGSLTRTTSTIDATDLTKY 169

Query: 155 DSVMASDVGNSTLNGTYENKM 175
           D+ MA+  G+ T+NG    K+
Sbjct: 170 DTAMAA--GDLTINGVDVGKI 188


  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
   0.309    0.124    0.335 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,591,215
Number of Sequences: 62578
Number of extensions: 471780
Number of successful extensions: 1226
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1208
Number of HSP's gapped (non-prelim): 28
length of query: 496
length of database: 14,973,337
effective HSP length: 103
effective length of query: 393
effective length of database: 8,527,803
effective search space: 3351426579
effective search space used: 3351426579
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 53 (25.0 bits)