TBLASTN 2.2.21 [Jun-14-2009]


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= AHPF_ECOLI Alkyl hydroperoxide reductase, F52a subunit,
FAD/NAD(P)-binding
         (521 letters)

Database: pm 
           204 sequences; 2,269,587 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE006093 Pasteurella multocida subsp. multocida str. Pm70 sectio...   148   7e-37
AE006163 Pasteurella multocida subsp. multocida str. Pm70 sectio...    50   3e-07

>AE006093 Pasteurella multocida subsp. multocida str. Pm70 section 60
            of 204 of the complete genome.
          Length = 10777

 Score =  148 bits (373), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 106/322 (32%), Positives = 166/322 (51%), Gaps = 13/322 (4%)
 Frame = -1

Query: 207  LNKRDAYDVLIVXXXXXXXXXXIYSARKGIRTGLM-GERFGGQILDTVDIENYIS-VPKT 264
            +N      +LI+          IY+AR  ++  L+ G + GGQ+  T +IEN+     +T
Sbjct: 1027 MNAMKHSQLLILGSGPAGYTAAIYAARANLKPVLVTGLQQGGQLTTTTEIENWPGDFGET 848

Query: 265  EGQKLAGALKVHVDEYDVDVI-DSQSASKLI--PAAVEGGLHQIETASGAVLKARSIIVA 321
             G +L   +  H +++D ++I D  +   L   P  + G +H             ++I+A
Sbjct: 847  TGPELMQRMLQHAEKFDTEIIFDHINKVDLSSRPFKLYGDVH--------TFSCDALIIA 692

Query: 322  TGAKWRNMNVPGEDQYRTKGVTYCPHCDGPLFKGKRVAVIGGGNSGVEAAIDLAGIVEHV 381
            TGA  R + +P E+ Y+ +GV+ C  CDG  ++ K VAVIGGGN+ VE A+ LA I   V
Sbjct: 691  TGASARYLGLPSEEAYKGRGVSACATCDGFFYRNKPVAVIGGGNTAVEEALYLANIASEV 512

Query: 382  TLLEFAPEMKADQVLQDKL-RSLKNVDIILNAQTT--EVKGDGSKVVGLEYRDRVSGDIH 438
             L+      +++++L D+L + ++   IIL+   T  EV GD   V G+  +D  S    
Sbjct: 511  HLVHRRDSFRSEKILIDRLMKKVEEGKIILHTNRTLDEVLGDNMGVTGVRLKDTQSEATE 332

Query: 439  NIELAGIFVQIGLLPNTNWLEGAVERNRMGEIIIDAKCE-----TNVKGVFAAGDCTTVP 493
             + L G+F+ IG  PNT+     +E N  G I++ +  E     T+V GVFAAGD     
Sbjct: 331  ELSLDGVFIAIGHAPNTDIFAEQLELNN-GYIVVKSGLEGNATATSVDGVFAAGDVMDHN 155

Query: 494  YKQIIIATGEGAKASLSAFDYL 515
            Y+Q I + G G  A+L A  YL
Sbjct: 154  YRQAITSAGTGCMAALDAERYL 89


>AE006163 Pasteurella multocida subsp. multocida str. Pm70 section 130
            of 204 of the complete genome.
          Length = 10823

 Score = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 62/218 (28%), Positives = 94/218 (43%), Gaps = 13/218 (5%)
 Frame = +3

Query: 309  SGAVLKARSIIVATGAKWRNMNVPGEDQYRTKGVTYCPHCDGPLFKG---KRVAVIGGGN 365
            +G  + A  I++ATG +  +  +PG +        Y    DG        KRVAV+G G 
Sbjct: 1428 NGEHITADHILIATGGRPSHPAIPGAE--------YGIDSDGVFALSELPKRVAVVGAGY 1583

Query: 366  SGVEAA--IDLAGIVEHVTLLEFAPEMKADQVLQDKLRSLKNVD-IILNAQTT--EV--K 418
              VE A  ++  G+  H+ + + AP    D ++ D L  +   D I L+ Q    EV   
Sbjct: 1584 IAVELAGVMNSFGVKTHLFVRQHAPLRHFDPLIVDTLLEVIQQDGIQLHTQAIPQEVVKN 1763

Query: 419  GDGSKVVGLEYRDRVSGDIHNIELAGIFVQIGLLPNT---NWLEGAVERNRMGEIIIDAK 475
             DGS  + LE       D  + E+  +   IG  P T   N     VE N  G + +D  
Sbjct: 1764 ADGSLTIKLE-------DGRSQEVDCLIWAIGRHPATDTINLEASGVETNARGFVKVDKY 1922

Query: 476  CETNVKGVFAAGDCTTVPYKQIIIATGEGAKASLSAFD 513
              TNV+G++A GD      +   +A   G + S   F+
Sbjct: 1923 QNTNVEGIYAVGDIIEGGIELTPVAVAAGRRLSERLFN 2036


  Database: pm
    Posted date:  Oct 27, 2009  5:14 PM
  Number of letters in database: 2,269,587
  Number of sequences in database:  204
  
Lambda     K      H
   0.316    0.135    0.386 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 204
Number of Hits to DB: 1,031,343
Number of extensions: 13155
Number of successful extensions: 61
Number of sequences better than 1.0e-03: 2
Number of HSP's gapped: 58
Number of HSP's successfully gapped: 2
Length of query: 521
Length of database: 756,529
Length adjustment: 86
Effective length of query: 435
Effective length of database: 738,985
Effective search space: 321458475
Effective search space used: 321458475
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 47 (22.7 bits)