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= 012265
         (467 letters)

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

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



>pdb|3IFZ|A Chain A, Crystal Structure Of The First Part Of The Mycobacterium
           Tuberculosis Dna Gyrase Reaction Core: The Breakage And
           Reunion Domain At 2.7 A Resolution
 pdb|3IFZ|B Chain B, Crystal Structure Of The First Part Of The Mycobacterium
           Tuberculosis Dna Gyrase Reaction Core: The Breakage And
           Reunion Domain At 2.7 A Resolution
          Length = 508

 Score = 32.3 bits (72), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 8/70 (11%)

Query: 243 LDSAIKWWLNAMTEDNKLSVIMQEAASFKLRHGREEDASHLFEELVKTHGSIEALVGLVT 302
           LD  I++++     D++L VI++   +++LR   E   +H+   LVK   +++ ++ L+ 
Sbjct: 358 LDQLIRYYV-----DHQLDVIVRRT-TYRLRKANER--AHILRGLVKALDALDEVIALIR 409

Query: 303 TSAHVDVDKA 312
            S  VD+ +A
Sbjct: 410 ASETVDIARA 419


>pdb|3ILW|A Chain A, Structure Of Dna Gyrase Subunit A N-Terminal Domain
 pdb|3ILW|B Chain B, Structure Of Dna Gyrase Subunit A N-Terminal Domain
          Length = 470

 Score = 32.0 bits (71), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 19/70 (27%), Positives = 40/70 (57%), Gaps = 8/70 (11%)

Query: 243 LDSAIKWWLNAMTEDNKLSVIMQEAASFKLRHGREEDASHLFEELVKTHGSIEALVGLVT 302
           LD  I++++     D++L VI++   +++LR   E   +H+   LVK   +++ ++ L+ 
Sbjct: 328 LDQLIRYYV-----DHQLDVIVRRT-TYRLRKANER--AHILRGLVKALDALDEVIALIR 379

Query: 303 TSAHVDVDKA 312
            S  VD+ +A
Sbjct: 380 ASETVDIARA 389


>pdb|2GW1|A Chain A, Crystal Structure Of The Yeast Tom70
 pdb|2GW1|B Chain B, Crystal Structure Of The Yeast Tom70
          Length = 514

 Score = 30.4 bits (67), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 16/70 (22%), Positives = 32/70 (45%)

Query: 119 AIYANRVLLLLHANKMDQARELVAALPDMFPDSVMPLLLQAAVLVRENKAGKAEELLGQF 178
           ++Y +R  +       DQA +      ++ P+++ P +  A +  RENK    E L  + 
Sbjct: 305 SVYYHRGQMNFILQNYDQAGKDFDKAKELDPENIFPYIQLACLAYRENKFDDCETLFSEA 364

Query: 179 AEKLPDKSKI 188
             K P+  ++
Sbjct: 365 KRKFPEAPEV 374


>pdb|1PG5|A Chain A, Crystal Structure Of The Unligated (t-state) Aspartate
           Transcarbamoylase From The Extremely Thermophilic
           Archaeon Sulfolobus Acidocaldarius
          Length = 299

 Score = 28.9 bits (63), Expect = 6.4,   Method: Compositional matrix adjust.
 Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)

Query: 319 LKPLPGLNGVDVDSLEKTSGAKHVESASY 347
           L PLP +N +D   ++KT+ AK+ E ASY
Sbjct: 257 LHPLPRVNEID-RKVDKTTKAKYFEQASY 284


>pdb|2BE9|A Chain A, Crystal Structure Of The Ctp-Liganded (T-State) Aspartate
           Transcarbamoylase From The Extremely Thermophilic
           Archaeon Sulfolobus Acidocaldarius
          Length = 300

 Score = 28.9 bits (63), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 14/29 (48%), Positives = 20/29 (68%), Gaps = 1/29 (3%)

Query: 319 LKPLPGLNGVDVDSLEKTSGAKHVESASY 347
           L PLP +N +D   ++KT+ AK+ E ASY
Sbjct: 258 LHPLPRVNEID-RKVDKTTKAKYFEQASY 285


  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    0.132    0.363 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,167,025
Number of Sequences: 62578
Number of extensions: 360273
Number of successful extensions: 921
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 919
Number of HSP's gapped (non-prelim): 9
length of query: 467
length of database: 14,973,337
effective HSP length: 102
effective length of query: 365
effective length of database: 8,590,381
effective search space: 3135489065
effective search space used: 3135489065
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: 53 (25.0 bits)