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= 006975
         (623 letters)

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

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



>pdb|1JEQ|A Chain A, Crystal Structure Of The Ku Heterodimer
 pdb|1JEY|A Chain A, Crystal Structure Of The Ku Heterodimer Bound To Dna
          Length = 609

 Score =  232 bits (592), Expect = 4e-61,   Method: Compositional matrix adjust.
 Identities = 196/607 (32%), Positives = 309/607 (50%), Gaps = 43/607 (7%)

Query: 26  ATKEYVVYLVDASPKMFSTTCPAEDQTDETHFHIAVSCIAQSLKTQIINRLYDEVAICFF 85
           + ++ +++LVDAS  MF +   +ED+   T F +++ CI     ++II+   D +A+ F+
Sbjct: 33  SGRDSLIFLVDASKAMFESQ--SEDEL--TPFDMSIQCIQSVYISKIISSDRDLLAVVFY 88

Query: 86  NTRKKKNLQDLNAVFVFNVAEREQLDRPTARFIKEFDHIE-ESFEKEIGSQYGIVSGSRE 144
            T K KN  +   ++V      ++LD P A+ I E D  + +  +K      G   GS +
Sbjct: 89  GTEKDKNSVNFKNIYVL-----QELDNPGAKRILELDQFKGQQGQKRFQDMMG--HGS-D 140

Query: 145 NSLYNALWVAQGLLRKGSSKTADKRILLFTNEDDPFGSIKGAAKNDMTRTTMQRAKDAQD 204
            SL   LWV   L      K + KRI+LFTNED+P G+   +AK    RT   +A D +D
Sbjct: 141 YSLSEVLWVCANLFSDVQFKMSHKRIMLFTNEDNPHGN--DSAKASRART---KAGDLRD 195

Query: 205 LGISIELLPLSPPDEEFKVSHFYADMIGL-EGDDLALFMPSAGQKLEDMKDQLRKRMFSK 263
            GI ++L+ L  P   F +S FY D+I + E +DL +    +  KLED+  ++R +   K
Sbjct: 196 TGIFLDLMHLKKPGG-FDISLFYRDIISIAEDEDLRVHFEESS-KLEDLLRKVRAKETRK 253

Query: 264 RIVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPLKTE-RSFICADTGALMQ 322
           R + R+   +   + I +  Y L++  +      L   TN P+KT+ R+F  +  G L+ 
Sbjct: 254 RALSRLKLKLNKDIVISVGIYNLVQKALKPPPIKLYRETNEPVKTKTRTFNTSTGGLLLP 313

Query: 323 EPAKRFQPYKGENIKFSVQELSEIKRVSTGHLRLHGFKPLSYLKDYHNLRPSTFVFPSDK 382
              KR Q Y    I    +E  E+KR     L L GFKPL  LK +H LRPS FV+P + 
Sbjct: 314 SDTKRSQIYGSRQIILEKEETEELKRFDDPGLMLMGFKPLVLLKKHHYLRPSLFVYPEES 373

Query: 383 EVVGSTCIFIALHRSMLRLNRFAVAFYGNPSN--PRLVALVAQ-DEIVRAGGQVEPPGMH 439
            V+GS+ +F AL    L     A+  Y    N  P  VALV Q +E+     QV PPG  
Sbjct: 374 LVIGSSTLFSALLIKCLEKEVAALCRYTPRRNIPPYFVALVPQEEELDDQKIQVTPPGFQ 433

Query: 440 MIYLPYSDDIRPVEELHSDTDAVPRASDDEVKKAAALMKRIDLKDFSVCQFANPSLQRHY 499
           +++LP++DD R +      T+ +  A+ ++V K  A+++++    +    F NP LQ+H+
Sbjct: 434 LVFLPFADDKRKM----PFTEKI-MATPEQVGKMKAIVEKLRFT-YRSDSFENPVLQQHF 487

Query: 500 AVLQALALEEDDMPEIKDETVPDEEGM-ARPGVVKAVEEFKLSVYGDNYDEEGDVKV--- 555
             L+ALAL+  +  +  D T+P  E M  R G +  V+EFK  VY  +Y+ EG V     
Sbjct: 488 RNLEALALDLMEPEQAVDLTLPKVEAMNKRLGSL--VDEFKELVYPPDYNPEGKVTKRKH 545

Query: 556 -SEASRKRKAATENAAKECANYDWADLADKGKLKEMTVQELKLYLMAHNLSTTGRKETLI 614
            +E S  ++   E + +E   +       KG L + TV  LK    A+ L +  +K+ L+
Sbjct: 546 DNEGSGSKRPKVEYSEEELKTH-----ISKGTLGKFTVPMLKEACRAYGLKSGLKKQELL 600

Query: 615 SRILTHM 621
             +  H 
Sbjct: 601 EALTKHF 607


>pdb|3D3U|A Chain A, Crystal Structure Of 4-Hydroxybutyrate Coa-Transferase
           (Abft-2) From Porphyromonas Gingivalis. Northeast
           Structural Genomics Consortium Target Pgr26
          Length = 439

 Score = 30.4 bits (67), Expect = 3.0,   Method: Compositional matrix adjust.
 Identities = 29/102 (28%), Positives = 49/102 (48%), Gaps = 6/102 (5%)

Query: 210 ELLPLSPPDEEFKVSHFYADMIGLEGDDLALFM---PSAG-QKLEDMKD-QLRKRMFSKR 264
           E+LP +  D E ++    A +I  +GD L L +   P A  + LE  KD  +   MF+  
Sbjct: 186 EVLPPAGSDLELRIGQNCASLIK-DGDTLQLGIGGIPDAVLRALEGHKDLGIHTEMFTDG 244

Query: 265 IVKRISFIIANGLSIELNTYALIRPTVPGAITWLDSVTNHPL 306
           +++ I   I NG    L+   ++   + G+    D V N+P+
Sbjct: 245 VMRMIRKGIINGKKKTLHPEKVVTSLIFGSKELYDFVNNNPV 286


>pdb|2LCQ|A Chain A, Solution Structure Of The Endonuclease Nob1 From
           P.Horikoshii
          Length = 165

 Score = 28.9 bits (63), Expect = 8.2,   Method: Composition-based stats.
 Identities = 18/83 (21%), Positives = 41/83 (49%), Gaps = 11/83 (13%)

Query: 522 DEEGMARPGVVKAVEEFKLSVYGDNYDEEGDVKVSEASRKRKAATENAAKECANYDWADL 581
           D EG   P VV+ +++ +  ++ ++    G VK++E S++        AKE         
Sbjct: 25  DIEGYTTPSVVEEIKDRESKIFLESLISAGKVKIAEPSKESIDRIIQVAKE--------- 75

Query: 582 ADKGKLKEMTVQELKLYLMAHNL 604
              G++ E++  ++++  +A+ L
Sbjct: 76  --TGEVNELSKADIEVLALAYEL 96


  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    0.134    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,720,045
Number of Sequences: 62578
Number of extensions: 733281
Number of successful extensions: 1714
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1701
Number of HSP's gapped (non-prelim): 14
length of query: 623
length of database: 14,973,337
effective HSP length: 105
effective length of query: 518
effective length of database: 8,402,647
effective search space: 4352571146
effective search space used: 4352571146
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: 54 (25.4 bits)