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= psy961
         (118 letters)

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

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



>pdb|1GAX|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1GAX|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1IVS|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1IVS|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1IYW|A Chain A, Preliminary Structure Of Thermus Thermophilus Ligand-Free
           Valyl-Trna Synthetase
 pdb|1IYW|B Chain B, Preliminary Structure Of Thermus Thermophilus Ligand-Free
           Valyl-Trna Synthetase
          Length = 862

 Score = 34.7 bits (78), Expect = 0.015,   Method: Composition-based stats.
 Identities = 22/76 (28%), Positives = 33/76 (43%), Gaps = 4/76 (5%)

Query: 37  QASKVKVSPIDSWILSRLADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPV 96
           QA +   +  D ++ SRL+  V      ++  +        Y L   E CD YLE  KP 
Sbjct: 597 QAKEDTPTLADRFMRSRLSRGVEEITALYEALDLAQAAREVYELVWSEFCDWYLEAAKPA 656

Query: 97  MADGSLIEKANAARTL 112
           +  G+    A+  RTL
Sbjct: 657 LKAGN----AHTLRTL 668


>pdb|3IM1|A Chain A, Structure Of The C-Terminal Sec63 Unit Of Yeast Brr2,
           P212121 Form
 pdb|3IM2|A Chain A, Structure Of The C-Terminal Sec63 Unit Of Yeast Brr2,
           P41212 Form
          Length = 328

 Score = 31.6 bits (70), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 24/37 (64%), Gaps = 2/37 (5%)

Query: 60  TCNKAFQKYE--FNTVTSACYNLWLYELCDVYLECIK 94
           T NK  Q+YE  F+T TS  +NL ++ +CD YL+  K
Sbjct: 283 TLNKETQQYELEFDTPTSGKHNLTIWCVCDSYLDADK 319


>pdb|3HIB|A Chain A, Crystal Structure Of The Second Sec63 Domain Of Yeast Brr2
          Length = 318

 Score = 31.6 bits (70), Expect = 0.12,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 24/37 (64%), Gaps = 2/37 (5%)

Query: 60  TCNKAFQKYE--FNTVTSACYNLWLYELCDVYLECIK 94
           T NK  Q+YE  F+T TS  +NL ++ +CD YL+  K
Sbjct: 273 TLNKETQQYELEFDTPTSGKHNLTIWCVCDSYLDADK 309


>pdb|2WOC|A Chain A, Crystal Structure Of The Dinitrogenase
           Reductase-Activating Glycohydrolase (Drag) From
           Rhodospirillum Rubrum
 pdb|2WOC|B Chain B, Crystal Structure Of The Dinitrogenase
           Reductase-Activating Glycohydrolase (Drag) From
           Rhodospirillum Rubrum
 pdb|2WOC|C Chain C, Crystal Structure Of The Dinitrogenase
           Reductase-Activating Glycohydrolase (Drag) From
           Rhodospirillum Rubrum
 pdb|2WOD|A Chain A, Crystal Structure Of The Dinitrogenase
           Reductase-Activating Glycohydrolase (Drag) From
           Rhodospirillum Rubrum In Complex With Adp-Ribsoyllysine
 pdb|2WOD|B Chain B, Crystal Structure Of The Dinitrogenase
           Reductase-Activating Glycohydrolase (Drag) From
           Rhodospirillum Rubrum In Complex With Adp-Ribsoyllysine
          Length = 299

 Score = 27.3 bits (59), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 10/31 (32%), Positives = 16/31 (51%)

Query: 49  WILSRLADAVATCNKAFQKYEFNTVTSACYN 79
           W+ SR  D   TC +  ++Y     T+A Y+
Sbjct: 95  WLKSRPVDVGNTCRRGIRRYMHEGTTTAPYS 125


>pdb|3TOS|A Chain A, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|B Chain B, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|C Chain C, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|D Chain D, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|E Chain E, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|F Chain F, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|G Chain G, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|H Chain H, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|I Chain I, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
 pdb|3TOS|J Chain J, Crystal Structure Of Cals11, Calicheamicin
           Methyltransferase
          Length = 257

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 13/49 (26%), Positives = 22/49 (44%)

Query: 55  ADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMADGSLI 103
            D   T  +   +     +  A ++L LYE     LE I+P +  GS++
Sbjct: 165 GDVRETVPRYLAENPQTVIALAYFDLDLYEPTKAVLEAIRPYLTKGSIV 213


>pdb|4GF5|A Chain A, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|C Chain C, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|E Chain E, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|F Chain F, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|H Chain H, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|B Chain B, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|D Chain D, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|G Chain G, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|I Chain I, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|J Chain J, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|K Chain K, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|L Chain L, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|M Chain M, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|N Chain N, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|O Chain O, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|P Chain P, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|Q Chain Q, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|R Chain R, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|S Chain S, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
 pdb|4GF5|T Chain T, Crystal Structure Of Calicheamicin Methyltransferase,
           Cals11
          Length = 257

 Score = 26.9 bits (58), Expect = 2.6,   Method: Compositional matrix adjust.
 Identities = 13/49 (26%), Positives = 22/49 (44%)

Query: 55  ADAVATCNKAFQKYEFNTVTSACYNLWLYELCDVYLECIKPVMADGSLI 103
            D   T  +   +     +  A ++L LYE     LE I+P +  GS++
Sbjct: 165 GDVRETVPRYLAENPQTVIALAYFDLDLYEPTKAVLEAIRPYLTKGSIV 213


>pdb|1BBT|1 Chain 1, Methods Used In The Structure Determination Of Foot And
          Mouth Disease Virus
 pdb|1FOD|1 Chain 1, Structure Of A Major Immunogenic Site On Foot-And-Mouth
          Disease Virus
          Length = 213

 Score = 25.4 bits (54), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 9  PYTHLTRWYGHVTELKKKQDADVNAALDQASKVKVSP 45
          P T     YG  T+++++Q  DV+  +D+   VKV+P
Sbjct: 10 PVTTTVENYGGETQIQRRQHTDVSFIMDRF--VKVTP 44


>pdb|1QQP|1 Chain 1, Foot-And-Mouth Disease Virus OLIGOSACCHARIDE RECEPTOR
          COMPLEX
          Length = 213

 Score = 25.4 bits (54), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 2/37 (5%)

Query: 9  PYTHLTRWYGHVTELKKKQDADVNAALDQASKVKVSP 45
          P T     YG  T+++++Q  DV+  +D+   VKV+P
Sbjct: 10 PVTTTVENYGGETQIQRRQHTDVSFIMDRF--VKVTP 44


  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
   0.320    0.130    0.396 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,205,392
Number of Sequences: 62578
Number of extensions: 100663
Number of successful extensions: 330
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 322
Number of HSP's gapped (non-prelim): 11
length of query: 118
length of database: 14,973,337
effective HSP length: 81
effective length of query: 37
effective length of database: 9,904,519
effective search space: 366467203
effective search space used: 366467203
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)