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= 025494
         (252 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 = 30.4 bits (67), Expect = 0.94,   Method: Compositional matrix adjust.
 Identities = 15/55 (27%), Positives = 29/55 (52%), Gaps = 6/55 (10%)

Query: 42  DLVRRGQLRSDRRGISRPLKYED------PFNNPLVKVGKSNSTMEMCGKVYRLA 90
           ++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 = 28.1 bits (61), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 59/152 (38%), Gaps = 29/152 (19%)

Query: 81  EMCGKVYRLAPITLTKEQQTIHQKRRSRA--YQWKRPTIFLKEGDLIPPDVDPDTVRWIP 138
            M GK     P+T   EQ   H   ++ A  Y+W            +  D  P+T  W+ 
Sbjct: 3   HMSGKARLHYPVTRQGEQ-VDHYFGQAVADPYRW------------LEDDRSPETEAWVK 49

Query: 139 ANHPFATTAN---------DIDEDLAQNNVYQKQGVPFRIRAEHEALQKKLEALQNEQKL 189
           A +  A T +          I E LA +  Y K+G PFR    H     K + LQN+  L
Sbjct: 50  AQN--AVTQDYLAQIPYRAAIKEKLAASWNYAKEGAPFREGRYHYFF--KNDGLQNQNVL 105

Query: 190 NKLVIDSSNAKDFERAFKLNPKSEEPLDQNPF 221
            +   +   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 = 28.1 bits (61), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 42/152 (27%), Positives = 59/152 (38%), Gaps = 29/152 (19%)

Query: 81  EMCGKVYRLAPITLTKEQQTIHQKRRSRA--YQWKRPTIFLKEGDLIPPDVDPDTVRWIP 138
            M GK     P+T   EQ   H   ++ A  Y+W            +  D  P+T  W+ 
Sbjct: 3   HMSGKARLHYPVTRQGEQ-VDHYFGQAVADPYRW------------LEDDRSPETEAWVK 49

Query: 139 ANHPFATTAN---------DIDEDLAQNNVYQKQGVPFRIRAEHEALQKKLEALQNEQKL 189
           A +  A T +          I E LA +  Y K+G PFR    H     K + LQN+  L
Sbjct: 50  AQN--AVTQDYLAQIPYRAAIKEKLAASWNYAKEGAPFREGRYHYFF--KNDGLQNQNVL 105

Query: 190 NKLVIDSSNAKDFERAFKLNPKSEEPLDQNPF 221
            +   +   A+ F     L+P     LDQ  F
Sbjct: 106 WRQQ-EGKPAEVFLDPNTLSPDGTTALDQLSF 136


>pdb|1O7D|D Chain D, The Structure Of The Bovine Lysosomal A-Mannosidase
           Suggests A Novel Mechanism For Low Ph Activation
          Length = 282

 Score = 27.3 bits (59), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 13/28 (46%), Positives = 17/28 (60%)

Query: 36  RPGSVEDLVRRGQLRSDRRGISRPLKYE 63
           R GS+E +V R  L+ D RG+  PL  E
Sbjct: 203 RDGSLELMVHRRLLKDDARGVGEPLNKE 230


  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    0.133    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,497,902
Number of Sequences: 62578
Number of extensions: 304485
Number of successful extensions: 815
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 813
Number of HSP's gapped (non-prelim): 9
length of query: 252
length of database: 14,973,337
effective HSP length: 97
effective length of query: 155
effective length of database: 8,903,271
effective search space: 1380007005
effective search space used: 1380007005
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: 50 (23.9 bits)