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= 042542
         (359 letters)

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

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



>pdb|4I1K|A Chain A, Crystal Structure Of Vrn1 (residues 208-341)
 pdb|4I1K|B Chain B, Crystal Structure Of Vrn1 (residues 208-341)
          Length = 146

 Score = 66.2 bits (160), Expect = 3e-11,   Method: Compositional matrix adjust.
 Identities = 36/115 (31%), Positives = 67/115 (58%), Gaps = 4/115 (3%)

Query: 246 MTLEEKQEAINVARFLKPEKPSFLVFLRASNMQLNCV-YVPNSFARKYFNG-EECVTIQD 303
           +T EE++ AIN A+  +P  P F V LR S +   C+ Y+P+ FA KY +G    + +Q 
Sbjct: 27  VTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQL 86

Query: 304 SDGRKLAVKVKVSCSKCLLTR-WGKFFKKTNVKEGDILFFEMIQMKNILLKVSVF 357
           ++ ++  V+      +   ++ W +F  + N+ EGD+  FE+++ ++ +LKV+ F
Sbjct: 87  AE-KQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDFVLKVTAF 140



 Score = 31.6 bits (70), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 29/110 (26%), Positives = 49/110 (44%), Gaps = 9/110 (8%)

Query: 12  ASSMKKTNSLFFQVILAVTIEDKK--MKIPQNFVGRFGDELS-YVATLTNPKGYVVRIGI 68
           A + + TN  FF+V+L  +   +   M +P  F  ++   +S ++      K + VR   
Sbjct: 39  AKTFEPTNP-FFRVVLRPSYLYRGCIMYLPSGFAEKYLSGISGFIKVQLAEKQWPVRC-- 95

Query: 69  TKKEGKIWFDDGWNEFVQYHSIGVGYFVVFQYRKNSKFQVFVFNTTTFEI 118
             K G+  F  GW EF   +++G G   VF+  +      FV   T F +
Sbjct: 96  LYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRD---FVLKVTAFRV 142


>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein
           At1g16640.1
          Length = 104

 Score = 31.2 bits (69), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 22/100 (22%), Positives = 41/100 (41%)

Query: 13  SSMKKTNSLFFQVILAVTIEDKKMKIPQNFVGRFGDELSYVATLTNPKGYVVRIGITKKE 72
            SM  T  + F          K ++IP  F   F         L +  G    + + K+ 
Sbjct: 1   GSMADTGEVQFMKPFISEKSSKSLEIPLGFNEYFPAPFPITVDLLDYSGRSWTVRMKKRG 60

Query: 73  GKIWFDDGWNEFVQYHSIGVGYFVVFQYRKNSKFQVFVFN 112
            K++   GW  FV+ +++  G ++ F Y ++  F V ++ 
Sbjct: 61  EKVFLTVGWENFVKDNNLEDGKYLQFIYDRDRTFYVIIYG 100


>pdb|3PJT|A Chain A, Structure Of Pseudomonas Fluorescence Lapd Eal Domain
           Complexed With C-Di-Gmp, C2221
 pdb|3PJT|B Chain B, Structure Of Pseudomonas Fluorescence Lapd Eal Domain
           Complexed With C-Di-Gmp, C2221
 pdb|3PJU|A Chain A, Structure Of Pseudomonas Fluorescence Lapd Eal Domain
           Complexed With C-Di-Gmp, P6522
          Length = 249

 Score = 27.7 bits (60), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 22/105 (20%), Positives = 48/105 (45%), Gaps = 2/105 (1%)

Query: 147 MQSKTYRMEELEVNDELDNVNDSIQDIIGTSNSEGSVHAKVHLSETQCLSVQETDLKIDS 206
           ++  T R+ EL  +  L         +IG     G  + K+  S  + +  QE+D ++  
Sbjct: 144 LEQLTRRLRELGFSLSLQRFGGRF-SMIGNLARLGLAYLKIDGSYIRAID-QESDKRLFI 201

Query: 207 TKFKKAKHNLKYELRADSVDQIKSIALLEDMDTYDCESRMTLEEK 251
              ++A H++   L A+ V+    ++++ +M  Y  + ++  E K
Sbjct: 202 EAIQRAAHSIDLPLIAERVETEGELSVIREMGLYGVQGQLFGEPK 246


  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    0.133    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,687,690
Number of Sequences: 62578
Number of extensions: 387833
Number of successful extensions: 1030
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1025
Number of HSP's gapped (non-prelim): 8
length of query: 359
length of database: 14,973,337
effective HSP length: 100
effective length of query: 259
effective length of database: 8,715,537
effective search space: 2257324083
effective search space used: 2257324083
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: 52 (24.6 bits)