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= 018589
         (353 letters)

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

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



>pdb|1O0W|A Chain A, Crystal Structure Of Ribonuclease Iii (Tm1102) From
           Thermotoga Maritima At 2.0 A Resolution
 pdb|1O0W|B Chain B, Crystal Structure Of Ribonuclease Iii (Tm1102) From
           Thermotoga Maritima At 2.0 A Resolution
          Length = 252

 Score = 45.4 bits (106), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 41/138 (29%), Positives = 64/138 (46%), Gaps = 22/138 (15%)

Query: 163 DTLLYLAFQHP--FCERNKA-RHVRAGHSRLCFLGQFVLELAFCEFFLQRYP-------- 211
           + LL+ A  H     E+N+A R     + +L FLG  VLEL  CE   ++YP        
Sbjct: 35  EELLFRALCHSSYANEQNQAGRKDVESNEKLEFLGDAVLELFVCEILYKKYPEAEVGDLA 94

Query: 212 RESPAPMRERVFGLIGRR-NLPKWIKAASLQNLIFPFDEMDRLIRKEREPPVKSVFWALF 270
           R   A   E V  ++ R+ NL K+         +F     ++   ++R+  +   F AL 
Sbjct: 95  RVKSAAASEEVLAMVSRKMNLGKF---------LFLGKGEEKTGGRDRDSILADAFEALL 145

Query: 271 GAIYLCFGFPEVYRVLFE 288
            AIYL  G+ ++ + LFE
Sbjct: 146 AAIYLDQGYEKI-KELFE 162


>pdb|2A11|A Chain A, Crystal Structure Of Nuclease Domain Of Ribonuclase Iii
           From Mycobacterium Tuberculosis
          Length = 242

 Score = 38.5 bits (88), Expect = 0.006,   Method: Compositional matrix adjust.
 Identities = 38/145 (26%), Positives = 55/145 (37%), Gaps = 11/145 (7%)

Query: 151 DQLGDDNPAKHFDTLLYLAFQH-PFCERNKARHVRAGHSRLCFLGQFVLELAFCEFFLQR 209
           D LG D P    D LL LA  H  +   N        + RL FLG  VL L   +    R
Sbjct: 12  DALGVDLP----DELLSLALTHRSYAYENGGLPT---NERLEFLGDAVLGLTITDALFHR 64

Query: 210 YPRESP---APMRERVFGLIGRRNLPKWIKAASLQNLIFPFDEMDRLIRKEREPPVKSVF 266
           +P  S    A +R  V       ++ + + A  L   +            ++   +    
Sbjct: 65  HPDRSEGDLAKLRASVVNTQALADVARRLCAEGLGVHVLLGRGEANTGGADKSSILADGM 124

Query: 267 WALFGAIYLCFGFPEVYRVLFEVFG 291
            +L GAIYL  G  +   V+  +FG
Sbjct: 125 ESLLGAIYLQHGMEKAREVILRLFG 149


  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
   0.323    0.139    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,719,745
Number of Sequences: 62578
Number of extensions: 322871
Number of successful extensions: 632
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 620
Number of HSP's gapped (non-prelim): 12
length of query: 353
length of database: 14,973,337
effective HSP length: 100
effective length of query: 253
effective length of database: 8,715,537
effective search space: 2205030861
effective search space used: 2205030861
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)