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= 025644
         (250 letters)

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

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



>pdb|3R9P|A Chain A, Crystal Structure Of Acka From Mycobacterium
           Paratuberculosis Atcc Baa-968  K-10
 pdb|3R9P|B Chain B, Crystal Structure Of Acka From Mycobacterium
           Paratuberculosis Atcc Baa-968  K-10
          Length = 391

 Score = 30.0 bits (66), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 25/100 (25%), Positives = 38/100 (38%), Gaps = 21/100 (21%)

Query: 103 HGAQSLRWFVWPNIDKDSIEMMSTECPRIIVNPKPSPFGFRGFEVPREAFPDI----TLD 158
           HG  +   F  P +  D++     E   +   P  +P   +G EV R   PDI      D
Sbjct: 87  HGGNT---FYRPTVLDDAVIARLHELSEL--APLHNPPALQGIEVARRLLPDIAHVAVFD 141

Query: 159 DPFVNDIDPSA------------WAVPRFASMGISTSLLS 186
             F +D+ P+A            W + R+   G S   +S
Sbjct: 142 TGFFHDLPPAAATYAIDRELADRWQIRRYGFHGTSHRYVS 181


>pdb|2H9A|B Chain B, Corrinoid Iron-Sulfur Protein
 pdb|2YCL|B Chain B, Complete Structure Of The Corrinoid,Iron-Sulfur Protein
           Including The N-Terminal Domain With A 4fe-4s Cluster
          Length = 310

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 2/38 (5%)

Query: 135 PKPSPFGFRGFEVPREAFPDITLDDPFVNDI-DPSAWA 171
           P P  F    F+ P   +PDI L +PF + I DP AWA
Sbjct: 44  PNPPRFALEVFDTPPTDWPDI-LVEPFKDVINDPVAWA 80


>pdb|3VMA|A Chain A, Crystal Structure Of The Full-Length Transglycosylase
           Pbp1b From Escherichia Coli
          Length = 768

 Score = 29.3 bits (64), Expect = 2.3,   Method: Composition-based stats.
 Identities = 34/131 (25%), Positives = 57/131 (43%), Gaps = 26/131 (19%)

Query: 28  QMCKSLKAVDISCCDRITAAGVSEFLLHCHSLETLRCGGSPRSNHAARRCLGILKPKLND 87
           +M K L+A       ++T  G  EF +  +S+E +R    P     ++   G ++ +L  
Sbjct: 87  EMVKLLEATQYRQVSKMTRPG--EFTVQANSIEMIR---RPFDFPDSKE--GQVRARLT- 138

Query: 88  VEGDSWEELVNTDIGHGAQSLRWFVWPNIDKDSIEMMSTECPRIIVNPKPSPFGFRGFEV 147
            +GD    +VN       ++ R F +  +D   I M+S            SP G +   V
Sbjct: 139 FDGDHLATIVNM------ENNRQFGFFRLDPRLITMIS------------SPNGEQRLFV 180

Query: 148 PREAFPDITLD 158
           PR  FPD+ +D
Sbjct: 181 PRSGFPDLLVD 191


>pdb|2P1M|B Chain B, Tir1-ask1 Complex Structure
 pdb|2P1N|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
 pdb|2P1N|E Chain E, Mechanism Of Auxin Perception By The Tir1 Ubiqutin Ligase
 pdb|2P1O|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|2P1P|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|2P1Q|B Chain B, Mechanism Of Auxin Perception By The Tir1 Ubiquitin Ligase
 pdb|3C6N|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
           Substrate Interactions In Auxin Perception And Signaling
 pdb|3C6O|B Chain B, Small Molecule Agonists And Antagonists Of F-Box
           Protein-Substrate Interactions In Auxin Perception And
           Signaling
 pdb|3C6P|B Chain B, Small Molecule Agonists And Antagonists Of F-Box Protein-
           Substrate Interactions In Auxin Perception And Signaling
          Length = 594

 Score = 29.3 bits (64), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 25/80 (31%), Positives = 37/80 (46%), Gaps = 6/80 (7%)

Query: 9   EILDISGSDVSDFGLVKVAQMCKSLKAVDISCCDRITAAGVSEFLLHCHSLETLRC--GG 66
           E+L ++ +  SD G+  V   C SL+ ++I  C      G    L +   LET+R     
Sbjct: 459 EMLSVAFAGDSDLGMHHVLSGCDSLRKLEIRDC----PFGDKALLANASKLETMRSLWMS 514

Query: 67  SPRSNHAARRCLGILKPKLN 86
           S   +  A + LG   PKLN
Sbjct: 515 SCSVSFGACKLLGQKMPKLN 534


  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
   0.320    0.135    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,957,700
Number of Sequences: 62578
Number of extensions: 278915
Number of successful extensions: 480
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 480
Number of HSP's gapped (non-prelim): 5
length of query: 250
length of database: 14,973,337
effective HSP length: 96
effective length of query: 154
effective length of database: 8,965,849
effective search space: 1380740746
effective search space used: 1380740746
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)