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= 008412
         (566 letters)

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

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



>pdb|1L1J|A Chain A, Crystal Structure Of The Protease Domain Of An Atp-
           Independent Heat Shock Protease Htra
 pdb|1L1J|B Chain B, Crystal Structure Of The Protease Domain Of An Atp-
           Independent Heat Shock Protease Htra
          Length = 239

 Score = 33.1 bits (74), Expect = 0.37,   Method: Compositional matrix adjust.
 Identities = 28/132 (21%), Positives = 54/132 (40%), Gaps = 14/132 (10%)

Query: 217 VAILGVSSYLKDLPNIALTPLNKR--GDLLLAVGSPFGVLSPMHFFNSVSMG--SVANCY 272
           +A++ + +  K  P +     +K   G+  +A+G+P G      F ++V++G  S  N  
Sbjct: 105 IAVIKIKASDKKFPYLEFGDSDKVKIGEWAIAIGNPLG------FQHTVTVGVVSATNRR 158

Query: 273 PPRSTTRS----LLMADIRCLPGMEGGPVFGEHAHFVGILIRPLRQKSGAEIQLVIPWEA 328
            P+         L+  D    PG  GGP+   H   +GI    +  +    +   IP   
Sbjct: 159 IPKPDGSGYYVGLIQTDAAINPGNSGGPLLNIHGEVIGINTAIVNPQEAVNLGFAIPINT 218

Query: 329 IATACSDLLLKE 340
           +      +L ++
Sbjct: 219 VKKFLDTILTQK 230


>pdb|4FLN|A Chain A, Crystal Structure Of Plant Protease Deg2
 pdb|4FLN|B Chain B, Crystal Structure Of Plant Protease Deg2
 pdb|4FLN|C Chain C, Crystal Structure Of Plant Protease Deg2
          Length = 539

 Score = 33.1 bits (74), Expect = 0.43,   Method: Compositional matrix adjust.
 Identities = 32/125 (25%), Positives = 51/125 (40%), Gaps = 11/125 (8%)

Query: 217 VAILGVSS--YLKDLPNIALTPLNKRGDLLLAVGSPFGVLSPMHFFNSVSMGSVA----N 270
           +A+L V S  + K    + L  L +  D +  VG P G  +      SV+ G V+     
Sbjct: 123 IALLSVESEDFWKGAEPLRLGHLPRLQDSVTVVGYPLGGDTI-----SVTKGVVSRIEVT 177

Query: 271 CYPPRSTTRSLLMADIRCLPGMEGGPVFGEHAHFVGILIRPLRQKSGAEIQLVIPWEAIA 330
            Y   S+    +  D    PG  GGP F +    +G+  +  R +    I  VIP   ++
Sbjct: 178 SYAHGSSDLLGIQIDAAINPGNSGGPAFNDQGECIGVAFQVYRSEETENIGYVIPTTVVS 237

Query: 331 TACSD 335
              +D
Sbjct: 238 HFLTD 242


>pdb|1Y8T|A Chain A, Crystal Structure Of Rv0983 From Mycobacterium
           Tuberculosis- Proteolytically Active Form
 pdb|1Y8T|B Chain B, Crystal Structure Of Rv0983 From Mycobacterium
           Tuberculosis- Proteolytically Active Form
 pdb|1Y8T|C Chain C, Crystal Structure Of Rv0983 From Mycobacterium
           Tuberculosis- Proteolytically Active Form
 pdb|2Z9I|A Chain A, Crystal Structure Of Rv0983 From Mycobacterium
           Tuberculosis- Proteolytically Active Form
 pdb|2Z9I|B Chain B, Crystal Structure Of Rv0983 From Mycobacterium
           Tuberculosis- Proteolytically Active Form
 pdb|2Z9I|C Chain C, Crystal Structure Of Rv0983 From Mycobacterium
           Tuberculosis- Proteolytically Active Form
          Length = 324

 Score = 30.0 bits (66), Expect = 3.5,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 35/84 (41%), Gaps = 10/84 (11%)

Query: 234 LTPLNKRGDLLLAVGSP-FGVLSPMHFFNSVSMGSVANCYPPRSTTR---------SLLM 283
           LTP++      L VG P   + SP+    +V+ G V+    P STT            + 
Sbjct: 100 LTPISLGSSSDLRVGQPVLAIGSPLGLEGTVTTGIVSALNRPVSTTGEAGNQNTVLDAIQ 159

Query: 284 ADIRCLPGMEGGPVFGEHAHFVGI 307
            D    PG  GG +   +A  VG+
Sbjct: 160 TDAAINPGNSGGALVNXNAQLVGV 183


>pdb|2HSG|A Chain A, Structure Of Transcription Regulator Ccpa In Its Dna-Free
           State
          Length = 332

 Score = 28.9 bits (63), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 34/136 (25%), Positives = 60/136 (44%), Gaps = 13/136 (9%)

Query: 262 SVSMGSVA---NCYPP-RSTTRSLLMADIRCL---PGMEGGPVFGEHAHFVGILIRPLRQ 314
           SVSM +V+   N  P  + +TR  ++  I  L   P      +  +    VG++I  +  
Sbjct: 13  SVSMATVSRVVNGNPNVKPSTRKKVLETIERLGYRPNAVARGLASKKTTTVGVIIPDISN 72

Query: 315 KSGAEIQLVIPWEAIATACSDLLLKEPQNAEKEIHINKGNLNAVGNSLLFNSHILNGACC 374
              AE+   I   A     + +L    QN +KE+H+    L    + ++F    ++G   
Sbjct: 73  IFYAELARGIEDIATMYKYNIILSNSDQNQDKELHLLNNMLGKQVDGIIF----MSGNVT 128

Query: 375 YKYEHVDSRCRSPLPI 390
              EHV+   +SP+P+
Sbjct: 129 --EEHVEELKKSPVPV 142


  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
   0.319    0.136    0.419 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,002,074
Number of Sequences: 62578
Number of extensions: 707339
Number of successful extensions: 1431
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: 1429
Number of HSP's gapped (non-prelim): 10
length of query: 566
length of database: 14,973,337
effective HSP length: 104
effective length of query: 462
effective length of database: 8,465,225
effective search space: 3910933950
effective search space used: 3910933950
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)