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= 021734
         (308 letters)

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

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



>pdb|3E0D|A Chain A, Insights Into The Replisome From The Crystral Structure Of
           The Ternary Complex Of The Eubacterial Dna Polymerase
           Iii Alpha-Subunit
 pdb|3E0D|B Chain B, Insights Into The Replisome From The Crystral Structure Of
           The Ternary Complex Of The Eubacterial Dna Polymerase
           Iii Alpha-Subunit
          Length = 1220

 Score = 28.1 bits (61), Expect = 6.0,   Method: Composition-based stats.
 Identities = 18/64 (28%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 124 GDDAQVEVGNYGDAAPWTPPQRTDSLEILTDFHLLAEEEKPLVSARFGHRKPIKSSPEDG 183
           G+D   ++G +G  A  +     D   +    H  AEE   L+  +FG  KP++ + E  
Sbjct: 485 GEDKVAQIGTFGSLA--SKAALKDVARVYGIPHKKAEELAKLIPVQFGKPKPLQEAFEAE 542

Query: 184 KKLR 187
            +LR
Sbjct: 543 PELR 546


>pdb|2V0P|A Chain A, The Structure Of Tap42 Alpha4 Subunit
 pdb|2V0P|B Chain B, The Structure Of Tap42 Alpha4 Subunit
          Length = 234

 Score = 27.7 bits (60), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 5/53 (9%)

Query: 231 VDPLLVKKSETFKDRTNFQLP-----PVNNSPGSAGKLRKEPSLSQDELNRRV 278
           +DPL+ +K   FKDR N QL      P NN   S  +L+++  +   + N+ +
Sbjct: 124 LDPLVGEKLGNFKDRYNPQLSELYAQPKNNKDLSGAQLKRKEKIELFQRNKEI 176


  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
   0.315    0.131    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,963,898
Number of Sequences: 62578
Number of extensions: 348103
Number of successful extensions: 865
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 865
Number of HSP's gapped (non-prelim): 3
length of query: 308
length of database: 14,973,337
effective HSP length: 99
effective length of query: 209
effective length of database: 8,778,115
effective search space: 1834626035
effective search space used: 1834626035
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)