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= psy15231
         (101 letters)

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

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



>pdb|4HE8|H Chain H, Crystal Structure Of The Membrane Domain Of Respiratory
          Complex I From Thermus Thermophilus
 pdb|4HE8|C Chain C, Crystal Structure Of The Membrane Domain Of Respiratory
          Complex I From Thermus Thermophilus
 pdb|4HEA|H Chain H, Crystal Structure Of The Entire Respiratory Complex I
          From Thermus Thermophilus
 pdb|4HEA|Q Chain Q, Crystal Structure Of The Entire Respiratory Complex I
          From Thermus Thermophilus
          Length = 365

 Score = 57.0 bits (136), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 31/90 (34%), Positives = 52/90 (57%), Gaps = 1/90 (1%)

Query: 10 PVDRNAMSGTESRTHTTTCEHSGVAFLTLLERKVLSFIQLRKGPNKRGVIGIFQPFSDAI 69
          PVD   M   ++         +  AF+TL+ER++L+  Q+R GPN+ G  G+ QP +DAI
Sbjct: 6  PVDPYWMVALKALL-VVVGLLTAFAFMTLIERRLLARFQVRMGPNRVGPFGLLQPLADAI 64

Query: 70 KLYTKEFFIPLKSNDYPYWVTPLISLGVSL 99
          K   KE  +  +++ + + + PLIS+  +L
Sbjct: 65 KSIFKEDIVVAQADRFLFVLAPLISVVFAL 94


>pdb|3DAQ|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
           Methicillin- Resistant Staphylococcus Aureus
 pdb|3DAQ|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
           Methicillin- Resistant Staphylococcus Aureus
 pdb|3DAQ|C Chain C, Crystal Structure Of Dihydrodipicolinate Synthase From
           Methicillin- Resistant Staphylococcus Aureus
 pdb|3DAQ|D Chain D, Crystal Structure Of Dihydrodipicolinate Synthase From
           Methicillin- Resistant Staphylococcus Aureus
          Length = 292

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 10/30 (33%), Positives = 20/30 (66%)

Query: 54  NKRGVIGIFQPFSDAIKLYTKEFFIPLKSN 83
           N+RG++  F+  +DA+KL    + +P ++N
Sbjct: 112 NQRGLVKHFEAIADAVKLPVVLYNVPSRTN 141


>pdb|3DI0|A Chain A, Crystal Structure Of Dihydrodipicolinate Synthase From
           Staphylococcus Aureus
 pdb|3DI0|B Chain B, Crystal Structure Of Dihydrodipicolinate Synthase From
           Staphylococcus Aureus
 pdb|3DI1|A Chain A, Crystal Structure Of The Staphylococcus Aureus
           Dihydrodipicolinate Synthase-pyruvate Complex
 pdb|3DI1|B Chain B, Crystal Structure Of The Staphylococcus Aureus
           Dihydrodipicolinate Synthase-pyruvate Complex
          Length = 295

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 10/30 (33%), Positives = 20/30 (66%)

Query: 54  NKRGVIGIFQPFSDAIKLYTKEFFIPLKSN 83
           N+RG++  F+  +DA+KL    + +P ++N
Sbjct: 113 NQRGLVKHFEAIADAVKLPVVLYNVPSRTN 142


>pdb|1XUU|A Chain A, Crystal Structure Of Sialic Acid Synthase (Neub) In
           Complex With Mn2+ And Malate From Neisseria Meningitidis
 pdb|1XUZ|A Chain A, Crystal Structure Analysis Of Sialic Acid Synthase
           (Neub)from Neisseria Meningitidis, Bound To Mn2+,
           Phosphoenolpyruvate, And N- Acetyl Mannosaminitol
 pdb|2ZDR|A Chain A, Crystal Structure Of Sialic Acid Synthase (Neub) From
           Neisseria Meningitidis In Complex With Mg2+ And (4s)-2-
           Methyl-2,4-Pentanediol
 pdb|3CM4|A Chain A, Crystal Structure Of Metal-Free Sialic Acid Synthase
           (Neub) From Neisseria Meningitidis In Complex With
           Malate
          Length = 349

 Score = 26.9 bits (58), Expect = 2.8,   Method: Composition-based stats.
 Identities = 24/80 (30%), Positives = 38/80 (47%), Gaps = 14/80 (17%)

Query: 30  HSGVAFLTLLERKVLSF---IQLRKGPNKRGVIGIFQPFSDAIKLYTKEFFIPL------ 80
           ++ V+   ++ER  L+    I+L++    +G+I I  PFS A  L  +   IP       
Sbjct: 74  NADVSIYEIMERCALNEEDEIKLKEYVESKGMIFISTPFSRAAALRLQRMDIPAYKIGSG 133

Query: 81  KSNDYPYWVTPLISLGVSLG 100
           + N+Y     PLI L  S G
Sbjct: 134 ECNNY-----PLIKLVASFG 148


  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
   0.322    0.140    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,039,400
Number of Sequences: 62578
Number of extensions: 102600
Number of successful extensions: 158
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: 155
Number of HSP's gapped (non-prelim): 4
length of query: 101
length of database: 14,973,337
effective HSP length: 67
effective length of query: 34
effective length of database: 10,780,611
effective search space: 366540774
effective search space used: 366540774
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 45 (21.9 bits)