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= 040770
         (521 letters)

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

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



>pdb|1PW4|A Chain A, Crystal Structure Of The Glycerol-3-Phosphate Transporter
           From E.Coli
          Length = 451

 Score = 39.7 bits (91), Expect = 0.005,   Method: Compositional matrix adjust.
 Identities = 45/187 (24%), Positives = 79/187 (42%), Gaps = 26/187 (13%)

Query: 96  TKTDVGNA--GVASVSGSIFSRLIMGAVCDLIGPRYGTSFLLLLSAPAVFCMSFVSDAQG 153
           ++ D+G A  G++   G  FS+ IMG+V D   PR      L+L+A  +  M FV  A  
Sbjct: 60  SRGDLGFALSGISIAYG--FSKFIMGSVSDRSNPRVFLPAGLILAAAVMLFMGFVPWATS 117

Query: 154 YIAARFMIGFCLATFV---------SCQYWTTIMFNGKILGLVNXXXXXXXXXXXXVTQL 204
            IA  F++ F    F          +  +W +    G I+ + N            V   
Sbjct: 118 SIAVMFVLLFLCGWFQGMGWPPCGRTMVHWWSQKERGGIVSVWN--------CAHNVGGG 169

Query: 205 LMPLVFEVIKLAGATPFTAWRIAFFIPGWLHVIMGILVLTLGQDLPDG-NLGALQKKGNV 263
           + PL+F    L G   F  W  A ++P +  +++ +    + +D P    L  +++  N 
Sbjct: 170 IPPLLF----LLGMAWFNDWHAALYMPAFCAILVALFAFAMMRDTPQSCGLPPIEEYKND 225

Query: 264 NKDKFSK 270
             D +++
Sbjct: 226 YPDDYNE 232


>pdb|1NSQ|A Chain A, Mechanism Of Phosphate Transfer By Nucleoside Diphosphate
           Kinase: X- Ray Structures Of A Phospho-Histidine
           Intermediate Of The Enzymes From Drosophila And
           Dictyostelium
 pdb|1NSQ|B Chain B, Mechanism Of Phosphate Transfer By Nucleoside Diphosphate
           Kinase: X- Ray Structures Of A Phospho-Histidine
           Intermediate Of The Enzymes From Drosophila And
           Dictyostelium
 pdb|1NSQ|C Chain C, Mechanism Of Phosphate Transfer By Nucleoside Diphosphate
           Kinase: X- Ray Structures Of A Phospho-Histidine
           Intermediate Of The Enzymes From Drosophila And
           Dictyostelium
          Length = 153

 Score = 29.3 bits (64), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 48  RAKAFKV----FSFAKPHMRTFHLAWVS---FFTCFISTFAAAPLVPIIRDNLNLTKTDV 100
             K FK+    F++A   +   H A +S   FF   ++   + P+VP++ + LN+ KT  
Sbjct: 30  EQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGR 89

Query: 101 GNAGVASVSGSIFSRLIMGAVCDLIG 126
              G  + + S+    I G  C  +G
Sbjct: 90  QMLGATNPADSL-PGTIRGDFCIQVG 114


>pdb|1NDL|A Chain A, The Awd Nucleotide Diphosphate Kinase From Drosophila
 pdb|1NDL|B Chain B, The Awd Nucleotide Diphosphate Kinase From Drosophila
 pdb|1NDL|C Chain C, The Awd Nucleotide Diphosphate Kinase From Drosophila
          Length = 153

 Score = 28.9 bits (63), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 8/86 (9%)

Query: 48  RAKAFKV----FSFAKPHMRTFHLAWVS---FFTCFISTFAAAPLVPIIRDNLNLTKTDV 100
             K FK+    F++A   +   H A +S   FF   ++   + P+VP++ + LN+ KT  
Sbjct: 30  EQKGFKLVALKFTWASKELLEKHYADLSARPFFPGLVNYMNSGPVVPMVWEGLNVVKTGR 89

Query: 101 GNAGVASVSGSIFSRLIMGAVCDLIG 126
              G  + + S+    I G  C  +G
Sbjct: 90  QMLGATNPADSL-PGTIRGDFCIQVG 114


  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
   0.327    0.140    0.437 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,257,514
Number of Sequences: 62578
Number of extensions: 498783
Number of successful extensions: 1110
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1108
Number of HSP's gapped (non-prelim): 3
length of query: 521
length of database: 14,973,337
effective HSP length: 103
effective length of query: 418
effective length of database: 8,527,803
effective search space: 3564621654
effective search space used: 3564621654
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 54 (25.4 bits)