TBLASTN 2.2.25 [Feb-01-2011]


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= PYRC_ECOLI P05020 Dihydroorotase (DHOase) (3.5.2.3)
         (348 letters)

Database: st 
           220 sequences; 4,870,572 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE008750 AE006468 Salmonella typhimurium LT2, section 54 of 220 ...   641   0.0  

>AE008750 AE006468 Salmonella typhimurium LT2, section 54 of 220 of the
             complete genome.
          Length = 20396

 Score =  641 bits (1653), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 300/348 (86%), Positives = 323/348 (92%)
 Frame = -1

Query: 1     MTAPSQVLKIRRPDDWHLHLRDGDMLKTVVPYTSEIYGRAIVMPNLXXXXXXXXXXXXYR 60
             MTAPSQVLKIRRPDDWH+HLRDGDMLKTVVPYTSEIYGRAIVMPNL            YR
Sbjct: 13349 MTAPSQVLKIRRPDDWHVHLRDGDMLKTVVPYTSEIYGRAIVMPNLASPITTVDAAIAYR 13170

Query: 61    QRILDAVPAGHDFTPLMTCYLTDSLDPNELERGFNEGVFTAAKLYPANATTNSSHGVTSI 120
             QRILDAVPAGHDFTPLMTCYLTDSLD +ELERGF+EGVFTAAKLYPANATTNSSHGVTS+
Sbjct: 13169 QRILDAVPAGHDFTPLMTCYLTDSLDADELERGFHEGVFTAAKLYPANATTNSSHGVTSV 12990

Query: 121   DAIMPVLERMEKIGMPLLVHGEVTHADIDIFDREARFIESVMEPLRQRLTALKVVFEHIT 180
             DAIMPVLERMEK+G+PLLVHGEVTHAD+DIFDREARFI++VMEPLRQRLTALKVVFEHIT
Sbjct: 12989 DAIMPVLERMEKLGIPLLVHGEVTHADVDIFDREARFIDTVMEPLRQRLTALKVVFEHIT 12810

Query: 181   TKDAADYVRDGNERLAATITPQHLMFNRNHMLVGGVRPHLYCLPILKRNIHQQALRELVA 240
             TKDAA YVRDGN+ LAATITPQHLMFNRN MLVGG+RPHLYCLPILKRNIHQQALRELVA
Sbjct: 12809 TKDAAQYVRDGNDYLAATITPQHLMFNRNDMLVGGIRPHLYCLPILKRNIHQQALRELVA 12630

Query: 241   SGFNRVFLGTDSAPHARHRKESSCGCAGCFNAPTALGSYATVFEEMNALQHFEAFCSVNG 300
             SGF R FLGTDSAPH+RHRKE+SCGCAGCFNAP+ALGSYA VFEEMNAL HFEAFCS+NG
Sbjct: 12629 SGFTRAFLGTDSAPHSRHRKETSCGCAGCFNAPSALGSYAAVFEEMNALAHFEAFCSLNG 12450

Query: 301   PQFYGLPVNDTFIELVREEQQVAESIALTDDTLVPFLAGETVRWSVKQ 348
             PQFYGLP+N  ++ELVR+EQQ+  +IAL DD+LVPFLAGETVRWSVK+
Sbjct: 12449 PQFYGLPMNTGWVELVRDEQQIPGNIALADDSLVPFLAGETVRWSVKK 12306


  Database: st
    Posted date:  Dec 26, 2011 11:05 PM
  Number of letters in database: 4,870,572
  Number of sequences in database:  220
  
Lambda     K      H
   0.322    0.137    0.412 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 220
Number of Hits to DB: 1,914,672
Number of extensions: 27357
Number of successful extensions: 173
Number of sequences better than 1.0e-03: 1
Number of HSP's gapped: 173
Number of HSP's successfully gapped: 1
Length of query: 348
Length of database: 1,623,524
Length adjustment: 88
Effective length of query: 260
Effective length of database: 1,604,164
Effective search space: 417082640
Effective search space used: 417082640
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)