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= 018859
         (349 letters)

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

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



>pdb|1VE5|A Chain A, Crystal Structure Of T.Th. Hb8 Threonine Deaminase
 pdb|1VE5|B Chain B, Crystal Structure Of T.Th. Hb8 Threonine Deaminase
 pdb|1VE5|C Chain C, Crystal Structure Of T.Th. Hb8 Threonine Deaminase
 pdb|1VE5|D Chain D, Crystal Structure Of T.Th. Hb8 Threonine Deaminase
          Length = 311

 Score = 30.8 bits (68), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 139 DLVRRGQLRSDRRGISRPLKYED------PFNNPLVKVGKSNSTMEMCGKVYRLA 187
           ++V RG    +R  ++R L+ E       PF++PLV  G+  + +E+  +  R+ 
Sbjct: 113 EVVDRGVTAKNREEVARALQEETGYALIHPFDDPLVIAGQGTAGLELLAQAGRMG 167


>pdb|3IUN|A Chain A, Appep_d622n Opened State
 pdb|3IUQ|A Chain A, Appep_d622n+pp Closed State
 pdb|3IUR|A Chain A, Appep_d266nx+h2h3 Opened State
          Length = 693

 Score = 27.7 bits (60), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 59/152 (38%), Gaps = 29/152 (19%)

Query: 178 EMCGKVYRLAPITLTKEQQTIHQKRRSRA--YQWKRPTIFLKEGDLIPPDVDPDTVRWIP 235
            M GK     P+T   EQ   H   ++ A  Y+W            +  D  P+T  W+ 
Sbjct: 3   HMSGKARLHYPVTRQGEQ-VDHYFGQAVADPYRW------------LEDDRSPETEAWVK 49

Query: 236 ANHPFATTAN---------DIDEDLAQNNVYQKQGVPFRIRAEHEALQKKLEALQNEQKL 286
           A +  A T +          I E LA +  Y K+G PFR    H     K + LQN+  L
Sbjct: 50  AQN--AVTQDYLAQIPYRAAIKEKLAASWNYAKEGAPFREGRYHYFF--KNDGLQNQNVL 105

Query: 287 NKLVIDSSNAKDFERAFKLNPKSEEPLDQNPF 318
            +   +   A+ F     L+P     LDQ  F
Sbjct: 106 WRQQ-EGKPAEVFLDPNTLSPDGTTALDQLSF 136


>pdb|3IUJ|A Chain A, Appep_wt2 Opened State
 pdb|3IUL|A Chain A, Appep_wt1 Opened State
 pdb|3IUM|A Chain A, Appep_wtx Opened State
          Length = 693

 Score = 27.7 bits (60), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 59/152 (38%), Gaps = 29/152 (19%)

Query: 178 EMCGKVYRLAPITLTKEQQTIHQKRRSRA--YQWKRPTIFLKEGDLIPPDVDPDTVRWIP 235
            M GK     P+T   EQ   H   ++ A  Y+W            +  D  P+T  W+ 
Sbjct: 3   HMSGKARLHYPVTRQGEQ-VDHYFGQAVADPYRW------------LEDDRSPETEAWVK 49

Query: 236 ANHPFATTAN---------DIDEDLAQNNVYQKQGVPFRIRAEHEALQKKLEALQNEQKL 286
           A +  A T +          I E LA +  Y K+G PFR    H     K + LQN+  L
Sbjct: 50  AQN--AVTQDYLAQIPYRAAIKEKLAASWNYAKEGAPFREGRYHYFF--KNDGLQNQNVL 105

Query: 287 NKLVIDSSNAKDFERAFKLNPKSEEPLDQNPF 318
            +   +   A+ F     L+P     LDQ  F
Sbjct: 106 WRQQ-EGKPAEVFLDPNTLSPDGTTALDQLSF 136


  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
   0.316    0.131    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,881,065
Number of Sequences: 62578
Number of extensions: 382802
Number of successful extensions: 943
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 941
Number of HSP's gapped (non-prelim): 10
length of query: 349
length of database: 14,973,337
effective HSP length: 100
effective length of query: 249
effective length of database: 8,715,537
effective search space: 2170168713
effective search space used: 2170168713
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)