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= psy16139
         (466 letters)

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

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



>pdb|1X3L|A Chain A, Crystal Structure Of The Ph0495 Protein From Pyrococccus
           Horikoshii Ot3
          Length = 440

 Score =  141 bits (355), Expect = 1e-33,   Method: Compositional matrix adjust.
 Identities = 110/305 (36%), Positives = 166/305 (54%), Gaps = 24/305 (7%)

Query: 4   IKLIYEAAVSAVNGQNLIQANVHLEKNKLIIRDQTVLIKNNVYLIGFGKAVLGMAVEIEA 63
           ++L+ EA + A +    +   V +  +K+I++ +   IK  VY+I  GKA   MA  IE 
Sbjct: 11  LRLVGEA-IKAADPYRAVLNAVKVSDDKIIVQGKEFEIKGKVYVIALGKAACEMARAIED 69

Query: 64  MFRPQRLKGILSVPFGSVGILKPQFNKN-SEIEIRECARNNLPDEASCQNTQLIQNFVKH 122
                    IL V  G V + K  + K    I++ E A + +PDE S    +   + +  
Sbjct: 70  ---------ILDVEDG-VAVTKYGYGKELKRIKVIE-AGHPIPDEKSILGAKEALSILNR 118

Query: 123 CTEDDVVLVLISGGGSACLSSPKSPLSLEDKLKTIKLLVQSGANIKELNKVRKKLSDVKG 182
             E+D+V +LISGGGSA    P+  +SLED   T  LL++SGA I E+N VRK +S VKG
Sbjct: 119 ARENDIVFILISGGGSALFELPEEGISLEDLKLTTDLLLKSGAKIHEINTVRKHISKVKG 178

Query: 183 GQLAEIVYPATLVSLIISDIVGDPLQDIASGPTVLNEDLWSDARDIVIKYGLQNKVSKSV 242
           G+LA+++   T + LIISD+VGD L+ IASGPTV +   + DA+ I+  Y +  KV +SV
Sbjct: 179 GKLAKMI-KGTGIVLIISDVVGDNLEAIASGPTVKDPTTFEDAKRILELYDIWEKVPESV 237

Query: 243 MTILSH-------ETPHQDTKYFENVHNHIIGNNRAALLGAKWKAESLGFQTVILSSDIE 295
              +         ET  +D     NVHN +I +N  +      +A+ LGF+  I+++ +E
Sbjct: 238 RLHIERGLRGEVEETLKED---LPNVHNFLIASNSISCEAIAREAQRLGFKAYIMTTTLE 294

Query: 296 GLGDD 300
           G   D
Sbjct: 295 GEAKD 299


>pdb|2B8N|A Chain A, Crystal Structure Of Glycerate Kinase (ec 2.7.1.31)
           (tm1585) From Thermotoga Maritima At 2.70 A Resolution
 pdb|2B8N|B Chain B, Crystal Structure Of Glycerate Kinase (ec 2.7.1.31)
           (tm1585) From Thermotoga Maritima At 2.70 A Resolution
          Length = 429

 Score =  133 bits (335), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 81/203 (39%), Positives = 122/203 (60%), Gaps = 7/203 (3%)

Query: 93  EIEIRECARNNLPDEASCQNTQLIQNFVKHCTEDDVVLVLISGGGSACLSSPKSPLSLED 152
           + EI E A + +PDE + + T+ +   V    E+D VL L+SGGGS+    P   +SLE+
Sbjct: 94  DFEIYE-AGHPVPDENTIKTTRRVLELVDQLNENDTVLFLLSGGGSSLFELPLEGVSLEE 152

Query: 153 KLKTIKLLVQSGANIKELNKVRKKLSDVKGGQLAEIVYPATLVSLIISDIVGDPLQDIAS 212
             K    L++SGA+I+E+N VRK LS VKGG+ AE V+PA +V+L++SD++GD L  IAS
Sbjct: 153 IQKLTSALLKSGASIEEINTVRKHLSQVKGGRFAERVFPAKVVALVLSDVLGDRLDVIAS 212

Query: 213 GPTVLNEDLWSDARDIVIKYGLQNKVSKSVMTILSHETPHQDTKYFENVHNHIIGNNRAA 272
           GP   +     DA  ++ KYG++   S+SV   +  ETP    K+  NV  H+IGN +  
Sbjct: 213 GPAWPDSSTSEDALKVLEKYGIET--SESVKRAILQETP----KHLSNVEIHLIGNVQKV 266

Query: 273 LLGAKWKAESLGFQTVILSSDIE 295
              AK  A+  GF   I+++ ++
Sbjct: 267 CDEAKSLAKEKGFNAEIITTSLD 289


  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
   0.318    0.135    0.378 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,127,261
Number of Sequences: 62578
Number of extensions: 465588
Number of successful extensions: 1200
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1194
Number of HSP's gapped (non-prelim): 5
length of query: 466
length of database: 14,973,337
effective HSP length: 102
effective length of query: 364
effective length of database: 8,590,381
effective search space: 3126898684
effective search space used: 3126898684
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (25.0 bits)