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= 038848
         (446 letters)

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

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



>pdb|2GMI|B Chain B, Mms2UBC13~UBIQUITIN
          Length = 137

 Score = 29.3 bits (64), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 291 GSDLGLPHVNP--RAYNIGSDL--ELPHANPRAYDVGSDLELPHVNPRAYDVGSDLGLPH 346
           G+ LG PH N   R Y++  D     P + P+   + S + LP VNP   +V +D     
Sbjct: 43  GTILGPPHSNHENRIYSLSIDCGPNYPDSPPKVTFI-SKINLPCVNPTTGEVQTDFHTLR 101

Query: 347 GSPRAYNIGS---DLRLPCGNP 365
              RAY + +   DLR     P
Sbjct: 102 DWKRAYTMETLLLDLRKEMATP 123


>pdb|1JAT|B Chain B, Mms2UBC13 UBIQUITIN CONJUGATING ENZYME COMPLEX
          Length = 138

 Score = 29.3 bits (64), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 26/82 (31%), Positives = 37/82 (45%), Gaps = 8/82 (9%)

Query: 291 GSDLGLPHVNP--RAYNIGSDL--ELPHANPRAYDVGSDLELPHVNPRAYDVGSDLGLPH 346
           G+ LG PH N   R Y++  D     P + P+   + S + LP VNP   +V +D     
Sbjct: 44  GTILGPPHSNHENRIYSLSIDCGPNYPDSPPKVTFI-SKINLPCVNPTTGEVQTDFHTLR 102

Query: 347 GSPRAYNIGS---DLRLPCGNP 365
              RAY + +   DLR     P
Sbjct: 103 DWKRAYTMETLLLDLRKEMATP 124


  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
   0.313    0.131    0.391 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,276,562
Number of Sequences: 62578
Number of extensions: 518629
Number of successful extensions: 769
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 761
Number of HSP's gapped (non-prelim): 11
length of query: 446
length of database: 14,973,337
effective HSP length: 102
effective length of query: 344
effective length of database: 8,590,381
effective search space: 2955091064
effective search space used: 2955091064
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (25.0 bits)