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= 038109
         (324 letters)

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

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



>pdb|2HS5|A Chain A, Structural Genomics, The Crystal Structure Of A Putative
           Transcriptional Regulator Gntr From Rhodococcus Sp. Rha1
          Length = 239

 Score = 28.5 bits (62), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 36/140 (25%), Positives = 55/140 (39%), Gaps = 30/140 (21%)

Query: 116 LKKIDEALRVVD----IMAEGGFGLSAITFHPILSVLTRGKRMEEAWGLMEVMKEIRVSP 171
           L ++ EAL + D    +    G G + I FH  L+ L    R++E      V  E R+  
Sbjct: 124 LSRVAEALDLADERYAVEDWTGVGTADIHFHSALASLNNSNRIDEL--XRSVWNEARL-- 179

Query: 172 DLTAYNYLLTAYCFKGNLTATSGVLKKMEEEKLGADARTYDALVLGACRAGRVEEAFVLL 231
               ++    A+ F G        L +  E         YDAL      AG  E A  LL
Sbjct: 180 ---VFHVXDDAHRFHGPY------LTRNHE--------IYDALA-----AGNTEAAGQLL 217

Query: 232 RRMVDDGQSVLYSTYAHVMG 251
           +  ++D ++ +   Y  V G
Sbjct: 218 KTYLEDAEAQILGAYRPVSG 237


>pdb|1SZU|A Chain A, The Structure Of Gamma-Aminobutyrate Aminotransferase
           Mutant: V241a
 pdb|1SZU|B Chain B, The Structure Of Gamma-Aminobutyrate Aminotransferase
           Mutant: V241a
 pdb|1SZU|C Chain C, The Structure Of Gamma-Aminobutyrate Aminotransferase
           Mutant: V241a
 pdb|1SZU|D Chain D, The Structure Of Gamma-Aminobutyrate Aminotransferase
           Mutant: V241a
          Length = 426

 Score = 28.1 bits (61), Expect = 6.1,   Method: Compositional matrix adjust.
 Identities = 28/128 (21%), Positives = 50/128 (39%), Gaps = 10/128 (7%)

Query: 122 ALRVVDIMAEGGFGLSAITF----------HPILSVLTRGKRMEEAWGLMEVMKEIRVSP 171
           A+ +  +  EGGF  S+  F          H I+ +    +      G +  M+++ V+P
Sbjct: 202 AIVIEPVQGEGGFYASSPAFMQRLRALCDEHGIMLIADEAQSGAGRTGTLFAMEQMGVAP 261

Query: 172 DLTAYNYLLTAYCFKGNLTATSGVLKKMEEEKLGADARTYDALVLGACRAGRVEEAFVLL 231
           DLT +   +        +T  + V+  +    LG          + A    +V E   LL
Sbjct: 262 DLTTFAKSIAGGFPLAGVTGRAEVMDAVAPGGLGGTYAGNPIACVAALEVLKVFEQENLL 321

Query: 232 RRMVDDGQ 239
           ++  D GQ
Sbjct: 322 QKANDLGQ 329


>pdb|1BRW|B Chain B, The Crystal Structure Of Pyrimidine Nucleoside
           Phosphorylase In A Closed Conformation
 pdb|1BRW|A Chain A, The Crystal Structure Of Pyrimidine Nucleoside
           Phosphorylase In A Closed Conformation
          Length = 433

 Score = 27.7 bits (60), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 40/135 (29%), Positives = 60/135 (44%), Gaps = 17/135 (12%)

Query: 180 LTAYCFKGNLTATSGVLKKMEEEKLGADARTYDALVLGACRAGRVEEAFVLLRRMVDDGQ 239
           +TA      L A+S + KK+     GADA   D          +++EA  L R MVD G+
Sbjct: 170 VTATVNSIPLIASSIMSKKIAA---GADAIVLDVKTGAGAFMKKLDEARRLARVMVDIGK 226

Query: 240 SVLYSTYAHVMGALLRLGYYA-------QAVKFVMVCGGRDIKLDTELFGSLGSKLIGLE 292
            V   T A +      LGY         +A++ +   G  D+   TEL  +LGS ++ L 
Sbjct: 227 RVGRRTMAVISDMSQPLGYAVGNALEVKEAIETLKGNGPHDL---TELCLTLGSHMVYLA 283

Query: 293 R----FNEANFILKE 303
                 +EA  +L+E
Sbjct: 284 EKAPSLDEARRLLEE 298


  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
   0.323    0.139    0.401 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,728,902
Number of Sequences: 62578
Number of extensions: 333909
Number of successful extensions: 739
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 736
Number of HSP's gapped (non-prelim): 7
length of query: 324
length of database: 14,973,337
effective HSP length: 99
effective length of query: 225
effective length of database: 8,778,115
effective search space: 1975075875
effective search space used: 1975075875
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)