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= 008236
         (573 letters)

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

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



>pdb|2A1R|A Chain A, Crystal Structure Of Parn Nuclease Domain
 pdb|2A1R|B Chain B, Crystal Structure Of Parn Nuclease Domain
 pdb|2A1S|A Chain A, Crystal Structure Of Native Parn Nuclease Domain
 pdb|2A1S|B Chain B, Crystal Structure Of Native Parn Nuclease Domain
 pdb|2A1S|C Chain C, Crystal Structure Of Native Parn Nuclease Domain
 pdb|2A1S|D Chain D, Crystal Structure Of Native Parn Nuclease Domain
          Length = 430

 Score = 80.9 bits (198), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 78/333 (23%), Positives = 140/333 (42%), Gaps = 51/333 (15%)

Query: 1   MDFLAKYQFDFNACIHEGVSYLSREQEDKALKHVNSTYEDESLDSWHSLKEIRDTHLFNI 60
           +DFLA   FDFN     G+ YL++E+E +  +  +   E  S  +          +    
Sbjct: 113 IDFLASQGFDFNKVFRNGIPYLNQEEERQLREQYD---EKRSQANGAGALSYVSPNTSKC 169

Query: 61  PDILFAERMK--DRLSEWLGGLLRNRDEGS-EVQPSFNDSKQQFETIFFKMRPAISLNGF 117
           P  +  ++ K  D++ E +  LL++ +  + +++P                       GF
Sbjct: 170 PVTIPEDQKKFIDQVVEKIEDLLQSEENKNLDLEPC---------------------TGF 208

Query: 118 TSHQLLLIQLVVRKHFKDLAYLRVSGENSCSQNVIVYIESESDKKMLMKEVKDEQKIDAE 177
              + L+ Q +  K+ K +    +  E      VI  ++ E  K+   ++   EQ+    
Sbjct: 209 --QRKLIYQTLSWKYPKGIHVETLETEKKERYIVISKVDEEERKRREQQKHAKEQE---- 262

Query: 178 MSIKASIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPH 237
             +  ++GF  VI  +++  KL++GHN  LD+ H   +F+ PLP    EF       FP 
Sbjct: 263 -ELNDAVGFSRVIHAIANSGKLVIGHNMLLDVMHTVHQFYCPLPADLSEFKEMTTCVFPR 321

Query: 238 IIDTKILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVE-VDD 296
           ++DTK++ +                ++ F  +    +L      L   P    +VE  + 
Sbjct: 322 LLDTKLMAS----------------TQPFKDIINNTSLAELEKRLKETPFNPPKVESAEG 365

Query: 297 IRSSNWNSGVKHEAGYDAFMTGCVFAQACSHLG 329
             S +  S   HEAGYDA++TG  F    ++LG
Sbjct: 366 FPSYDTASEQLHEAGYDAYITGLCFISMANYLG 398


>pdb|3D45|A Chain A, Crystal Structure Of Mouse Parn In Complex With M7gpppg
 pdb|3D45|B Chain B, Crystal Structure Of Mouse Parn In Complex With M7gpppg
          Length = 507

 Score = 75.5 bits (184), Expect = 8e-14,   Method: Compositional matrix adjust.
 Identities = 66/261 (25%), Positives = 112/261 (42%), Gaps = 37/261 (14%)

Query: 183 SIGFRHVIDLLSSEKKLIVGHNCFLDIAHIYSKFFGPLPLTAEEFISSVNKYFPHIIDTK 242
           ++GF  VI  +++  KL+VGHN  LD+ H   +F+ PLP    EF       FP ++DTK
Sbjct: 262 AVGFSRVIHAIANSGKLVVGHNMLLDVMHTIHQFYCPLPADLNEFKEMAICVFPRLLDTK 321

Query: 243 ILLNSNSILQQRMKKSSTSLSKAFSVLCPQIALGSKSTHLALQPSVKVEVE-VDDIRSSN 301
           ++ +                ++ F  +    +L      L   P    +VE  +   S +
Sbjct: 322 LMAS----------------TQPFKDIINNTSLAELEKRLKETPFDPPKVESAEGFPSYD 365

Query: 302 WNSGVKHEAGYDAFMTGCVFAQACSHLGIDFKQQSSSENLAHNEKLREHVNLLYLSWTNG 361
             S   HEAGYDA++TG  F    ++LG          + A ++ +    N L+L     
Sbjct: 366 TASEQLHEAGYDAYITGLCFISMANYLGSLLSPPKMCVS-ARSKLIEPFFNKLFLM---- 420

Query: 362 EIINLSTGNRTSESLASNKRKNHYPKILFECIVIVWGFPSHLKAWDIRECISKVYGPTSV 421
            ++++   N     L    +++H         V+   FP   K  D+ +  S  +G    
Sbjct: 421 RVMDIPYLNLEGPDL--QPKRDH---------VLHVTFPKEWKTSDLYQLFS-AFG---N 465

Query: 422 ISVYHVDETAVFVQFSRAEMV 442
           I +  +D+T+ FV  S+ E V
Sbjct: 466 IQISWIDDTSAFVSLSQPEQV 486



 Score = 32.0 bits (71), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 13/27 (48%), Positives = 18/27 (66%)

Query: 1   MDFLAKYQFDFNACIHEGVSYLSREQE 27
           +DFLA   FDFN     G+ YL++E+E
Sbjct: 115 IDFLASQGFDFNKVFCSGIPYLNQEEE 141


>pdb|4ECN|A Chain A, Crystal Structure Of A Leucine-Rich Repeat Protein
           (Bt_0210) From Bacteroides Thetaiotaomicron Vpi-5482 At
           2.80 A Resolution
          Length = 876

 Score = 28.9 bits (63), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 18/25 (72%), Gaps = 1/25 (4%)

Query: 38  YEDESLDSWHSLKEIRDTHLFNIPD 62
           YE+E L SW +LK++ D  L+N P+
Sbjct: 480 YENEEL-SWSNLKDLTDVELYNCPN 503


  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    0.132    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,064,475
Number of Sequences: 62578
Number of extensions: 642096
Number of successful extensions: 1419
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1413
Number of HSP's gapped (non-prelim): 8
length of query: 573
length of database: 14,973,337
effective HSP length: 104
effective length of query: 469
effective length of database: 8,465,225
effective search space: 3970190525
effective search space used: 3970190525
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)