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= psy3712
         (109 letters)

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

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



>pdb|3VU4|A Chain A, Crystal Structure Of Kluyvelomyces Marxianus Hsv2
 pdb|3VU4|B Chain B, Crystal Structure Of Kluyvelomyces Marxianus Hsv2
          Length = 355

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Composition-based stats.
 Identities = 37/93 (39%), Positives = 48/93 (51%), Gaps = 8/93 (8%)

Query: 5   FRIYNCDPLKEKERQDFTDGGLGHVEMLFRCNYLALVGGGTHPKYPNNRVMIWDDLKKQV 64
           F IYN  P+     Q+     L  V ML R NY+A V G          V IWDD+KKQ 
Sbjct: 42  FEIYNVHPVAHIMSQEMRH--LSKVRMLHRTNYVAFVTG------VKEVVHIWDDVKKQD 93

Query: 65  VICLEFNAPVKGVRLRRDKIVVVLEGLIKVYTF 97
           V  ++ +APVK + L R+ IVV    +I V+ F
Sbjct: 94  VSRIKVDAPVKDLFLSREFIVVSYGDVISVFKF 126


>pdb|4AV8|A Chain A, Kluyveromyces Lactis Hsv2 Complete Loop 6cd
 pdb|4AV9|A Chain A, Kluyveromyces Lactis Hsv2
 pdb|4EXV|A Chain A, Structure Of Kluyveromyces Lactis Hsv2p
          Length = 339

 Score = 55.8 bits (133), Expect = 7e-09,   Method: Composition-based stats.
 Identities = 34/93 (36%), Positives = 48/93 (51%), Gaps = 8/93 (8%)

Query: 5   FRIYNCDPLKEKERQDFTDGGLGHVEMLFRCNYLALVGGGTHPKYPNNRVMIWDDLKKQV 64
           F IYN  PLK    Q+  D G   + ML R NY+A V            + IWDD+KKQ 
Sbjct: 37  FDIYNVHPLKRIMSQEMPDAGT--IRMLHRTNYIAFV------STKKELLHIWDDVKKQD 88

Query: 65  VICLEFNAPVKGVRLRRDKIVVVLEGLIKVYTF 97
           +  ++ +A VK + L R+ IVV    +I ++ F
Sbjct: 89  ITRVKLDAAVKDLFLSREFIVVSQGDVISIFKF 121


>pdb|13PK|A Chain A, Ternary Complex Of Phosphoglycerate Kinase From
          Trypanosoma Brucei
 pdb|13PK|B Chain B, Ternary Complex Of Phosphoglycerate Kinase From
          Trypanosoma Brucei
 pdb|13PK|C Chain C, Ternary Complex Of Phosphoglycerate Kinase From
          Trypanosoma Brucei
 pdb|13PK|D Chain D, Ternary Complex Of Phosphoglycerate Kinase From
          Trypanosoma Brucei
 pdb|16PK|A Chain A, Phosphoglycerate Kinase From Trypanosoma Brucei
          Bisubstrate Analog
          Length = 415

 Score = 26.9 bits (58), Expect = 3.3,   Method: Composition-based stats.
 Identities = 18/40 (45%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 59 DLK-KQVVICLEFNAPVKGVRLRRD-KIVVVLEGLIKVYT 96
          DLK K+V+I ++FN PVK  ++  D +I   L  L KV T
Sbjct: 9  DLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLT 48


>pdb|4DGT|A Chain A, Crystal Structure Of Plp-Bound Putative Aminotransferase
           From Clostridium Difficile 630 Crystallized With
           Magnesium Formate
 pdb|4DGT|B Chain B, Crystal Structure Of Plp-Bound Putative Aminotransferase
           From Clostridium Difficile 630 Crystallized With
           Magnesium Formate
 pdb|4DQ6|A Chain A, Crystal Structure Of Plp-Bound Putative Aminotransferase
           From Clostridium Difficile 630
 pdb|4DQ6|B Chain B, Crystal Structure Of Plp-Bound Putative Aminotransferase
           From Clostridium Difficile 630
          Length = 391

 Score = 25.8 bits (55), Expect = 7.1,   Method: Composition-based stats.
 Identities = 14/40 (35%), Positives = 20/40 (50%)

Query: 46  HPKYPNNRVMIWDDLKKQVVICLEFNAPVKGVRLRRDKIV 85
           +P  P  RV   D+LKK   ICL+ N  +    +  D I+
Sbjct: 172 NPHNPVGRVWTKDELKKLGDICLKHNVKIISDEIHSDIIL 211


  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
   0.327    0.147    0.470 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,627,949
Number of Sequences: 62578
Number of extensions: 140570
Number of successful extensions: 298
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 293
Number of HSP's gapped (non-prelim): 5
length of query: 109
length of database: 14,973,337
effective HSP length: 73
effective length of query: 36
effective length of database: 10,405,143
effective search space: 374585148
effective search space used: 374585148
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 45 (21.9 bits)