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= 040358
         (236 letters)

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

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



>pdb|4DWR|B Chain B, Rna Ligase RtcbMN2+ COMPLEX
 pdb|4DWR|A Chain A, Rna Ligase RtcbMN2+ COMPLEX
 pdb|4DWR|C Chain C, Rna Ligase RtcbMN2+ COMPLEX
          Length = 487

 Score = 27.7 bits (60), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 62  SEGLGKLFEKGLISIVNLRL----IPWGNAKIVEPNKTIDCQHGEDECYFNTIEACAILA 117
           S GLG       + I+   +    IPW + ++V    ++  Q  E + YF+ ++A A  A
Sbjct: 237 SRGLGHQVASDYLRIMERAIRKYRIPWPDRELV----SVPFQSEEGQRYFSAMKAAANFA 292

Query: 118 WPDQ 121
           W ++
Sbjct: 293 WANR 296


>pdb|1UC2|A Chain A, Hypothetical Extein Protein Of Ph1602 From Pyrococcus
           Horikoshii
 pdb|1UC2|B Chain B, Hypothetical Extein Protein Of Ph1602 From Pyrococcus
           Horikoshii
 pdb|4DWQ|A Chain A, Rtcb-GmpMN2+ COMPLEX
 pdb|4DWQ|B Chain B, Rtcb-GmpMN2+ COMPLEX
          Length = 481

 Score = 27.7 bits (60), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 31/64 (48%), Gaps = 8/64 (12%)

Query: 62  SEGLGKLFEKGLISIVNLRL----IPWGNAKIVEPNKTIDCQHGEDECYFNTIEACAILA 117
           S GLG       + I+   +    IPW + ++V    ++  Q  E + YF+ ++A A  A
Sbjct: 237 SRGLGHQVASDYLRIMERAIRKYRIPWPDRELV----SVPFQSEEGQRYFSAMKAAANFA 292

Query: 118 WPDQ 121
           W ++
Sbjct: 293 WANR 296


  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
   0.321    0.140    0.457 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,808,028
Number of Sequences: 62578
Number of extensions: 337999
Number of successful extensions: 589
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 589
Number of HSP's gapped (non-prelim): 5
length of query: 236
length of database: 14,973,337
effective HSP length: 96
effective length of query: 140
effective length of database: 8,965,849
effective search space: 1255218860
effective search space used: 1255218860
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: 50 (23.9 bits)