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= 006565
         (640 letters)

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

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



>pdb|3KE6|A Chain A, The Crystal Structure Of The Rsbu And Rsbw Domains Of
           Rv1364c From Mycobacterium Tuberculosis
 pdb|3KE6|B Chain B, The Crystal Structure Of The Rsbu And Rsbw Domains Of
           Rv1364c From Mycobacterium Tuberculosis
          Length = 399

 Score = 31.2 bits (69), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 23/82 (28%), Positives = 36/82 (43%), Gaps = 15/82 (18%)

Query: 30  DNVVKVLDGLISEYETSCHGPGK--------WQKLATFLQQSSEGPILDLVKRLIDQIGS 81
           D ++   DGLI         PG+        +  LA  +   S G +LD   R ID++ S
Sbjct: 181 DAILFYTDGLIER-------PGRPLEASTAEFADLAASIASGSGGFVLDAPARPIDRLCS 233

Query: 82  ERSSLMLKYRSIEDNMKLLKKQ 103
           +   L+L+     D++ LL  Q
Sbjct: 234 DTLELLLRSTGYNDDVTLLAMQ 255


>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
            Domain
 pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein Motor
            Domain
          Length = 3245

 Score = 30.0 bits (66), Expect = 3.7,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)

Query: 144  ISLREKSSSLSKTVDSLKNEISDWKRKY--DQV 174
            I LR++  S SK VD ++   SDWK+ +  DQV
Sbjct: 2536 ICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQV 2568


>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
            Domain
 pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
            Domain
          Length = 3367

 Score = 30.0 bits (66), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 15/33 (45%), Positives = 21/33 (63%), Gaps = 2/33 (6%)

Query: 144  ISLREKSSSLSKTVDSLKNEISDWKRKY--DQV 174
            I LR++  S SK VD ++   SDWK+ +  DQV
Sbjct: 2658 ICLRQQVPSFSKLVDHIQQNSSDWKQFFGKDQV 2690


>pdb|4GF2|A Chain A, Crystal Structure Of Plasmodium Falciparum Erythrocyte
           Binding Antigen 140 (Pfeba-140BAEBL)
          Length = 615

 Score = 29.3 bits (64), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 43/160 (26%), Positives = 73/160 (45%), Gaps = 16/160 (10%)

Query: 26  DASIDNVVKVLDGLISEYETSCHGPGKWQKLATFLQQSSEGPILDLVKRLIDQIGS-ERS 84
           D + +NV KV+  ++   ET C    K+QK+  FL+   E    D  ++  ++I S E  
Sbjct: 447 DENKENVWKVMSAVLKNKET-CKDYDKFQKIPQFLRWFKEWGD-DFCEKRKEKIYSFESF 504

Query: 85  SLMLKYRSIEDNMKLLKKQLEDSERY----KSEYLKRYDDAINDKKKLADDYTSRINNLQ 140
            +  K +  ++N    K +  + +++    KSEY K+ D    DK K   D    + N +
Sbjct: 505 KVECKKKDCDENT--CKNKCSEYKKWIDLKKSEYEKQVDKYTKDKNKKMYDNIDEVKNKE 562

Query: 141 GENISLREKSSSL------SKTVDSLKNEISDWKRKYDQV 174
             N+ L+EKS          K  +   NE  D  +K D++
Sbjct: 563 A-NVYLKEKSKECKDVNFDDKIFNEAPNEYEDMCKKCDEI 601


  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
   0.309    0.124    0.325 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,813,141
Number of Sequences: 62578
Number of extensions: 417110
Number of successful extensions: 1264
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 37
Number of HSP's that attempted gapping in prelim test: 1238
Number of HSP's gapped (non-prelim): 61
length of query: 640
length of database: 14,973,337
effective HSP length: 105
effective length of query: 535
effective length of database: 8,402,647
effective search space: 4495416145
effective search space used: 4495416145
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 55 (25.8 bits)