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= 015251
         (410 letters)

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

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



>pdb|2OVP|B Chain B, Structure Of The Skp1-Fbw7 Complex
 pdb|2OVQ|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegc Complex
 pdb|2OVR|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegn Complex
          Length = 445

 Score = 36.2 bits (82), Expect = 0.035,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 23/37 (62%)

Query: 28 LPREIVLHILLRLPITSLVQFKFVCRAWRALAQDPLL 64
          LP+E+ L++L  L    L+Q    CR WR LA+D LL
Sbjct: 22 LPKELALYVLSFLEPKDLLQAAQTCRYWRILAEDNLL 58


>pdb|1BP1|A Chain A, Crystal Structure Of Bpi, The Human Bactericidal
           Permeability-Increasing Protein
          Length = 456

 Score = 33.5 bits (75), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 47/110 (42%), Gaps = 9/110 (8%)

Query: 112 PFQAKMPEFDAVGSCNGLLCLSDSLFNDAICIYNPFT------RDYIELPKSMQYPDQEV 165
           PF   + EF A       L LSD  FN A  +Y          RD + +PK  ++     
Sbjct: 238 PFAPPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDM-IPKESKFRLTTK 296

Query: 166 VFGFGFHPVSKEYKVIKIVYYRKSCS--NSSFQRTRRVIYPRSDVQVYTV 213
            FG     V+K++  +KI  +  + +  + S Q T    YP  DVQ + V
Sbjct: 297 FFGTFLPEVAKKFPNMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAV 346


>pdb|1EWF|A Chain A, The 1.7 Angstrom Crystal Structure Of Bpi
          Length = 456

 Score = 33.5 bits (75), Expect = 0.21,   Method: Compositional matrix adjust.
 Identities = 32/110 (29%), Positives = 47/110 (42%), Gaps = 9/110 (8%)

Query: 112 PFQAKMPEFDAVGSCNGLLCLSDSLFNDAICIYNPFT------RDYIELPKSMQYPDQEV 165
           PF   + EF A       L LSD  FN A  +Y          RD + +PK  ++     
Sbjct: 238 PFAPPVMEFPAAHDRMVYLGLSDYFFNTAGLVYQEAGVLKMTLRDDM-IPKESKFRLTTK 296

Query: 166 VFGFGFHPVSKEYKVIKIVYYRKSCS--NSSFQRTRRVIYPRSDVQVYTV 213
            FG     V+K++  +KI  +  + +  + S Q T    YP  DVQ + V
Sbjct: 297 FFGTFLPEVAKKFPNMKIQIHVSASTPPHLSVQPTGLTFYPAVDVQAFAV 346


>pdb|2OLS|A Chain A, The Crystal Structure Of The Phosphoenolpyruvate Synthase
           From Neisseria Meningitidis
          Length = 794

 Score = 30.4 bits (67), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 23/113 (20%), Positives = 53/113 (46%), Gaps = 8/113 (7%)

Query: 204 PRSDVQVY-TVGSPAWRSKGKLAYQFVRRPSEALVKGRLHWVTRPRRYSPVRGIVSFDIA 262
           P++ V+V   VG+P      +LA+ F   PSE +   R+ ++   +     + ++ FD  
Sbjct: 481 PKAPVKVMMNVGNP------ELAFSFANLPSEGIGLARMEFIINRQIGIHPKALLEFDKQ 534

Query: 263 DEQFR-EVPKPDCGGLNRCNYHLTVLSGCLSVAVYGNYGKLEIWVMKDYNVKE 314
           D++ + E+ +   G  +  ++++  ++  ++      Y +  I  M D+   E
Sbjct: 535 DDELKAEITRRIAGYASPVDFYVDKIAEGVATLAASVYPRKTIVRMSDFKSNE 587


>pdb|2KKN|A Chain A, Solution Nmr Structure Of Themotoga Maritima Protein
           Tm1076: Northeast Structural Genomics Consortium Target
           Vt57
          Length = 178

 Score = 30.0 bits (66), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 15/67 (22%), Positives = 35/67 (52%), Gaps = 4/67 (5%)

Query: 96  FIDFSDNQDKVRKFNMPFQAKMPEFDAVGSCNGLLCLSDSLFNDAICIYNPFTRDYIELP 155
           F+  SD+   VR  ++P +      +++   +G++ L D +  D + +   F++++  + 
Sbjct: 25  FLLISDSHVPVRMASLPDEI----LNSLKEYDGVIGLGDYVDLDTVILLEKFSKEFYGVH 80

Query: 156 KSMQYPD 162
            +M YPD
Sbjct: 81  GNMDYPD 87


  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
   0.323    0.139    0.438 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,883,118
Number of Sequences: 62578
Number of extensions: 547681
Number of successful extensions: 929
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 923
Number of HSP's gapped (non-prelim): 11
length of query: 410
length of database: 14,973,337
effective HSP length: 101
effective length of query: 309
effective length of database: 8,652,959
effective search space: 2673764331
effective search space used: 2673764331
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)