BLASTP 2.2.18 [Mar-02-2008]


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= 0002.0084.p
         (471 letters)

Database: BlastDatabases/689/689 
           4735 sequences; 1,619,870 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309795|ref|YP_003773887.1| DNA polymerase I protein [Herba...   936   0.0  

>gi|300309795|ref|YP_003773887.1| DNA polymerase I protein
           [Herbaspirillum seropedicae SmR1]
          Length = 920

 Score =  936 bits (2420), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 451/471 (95%), Positives = 463/471 (98%)

Query: 1   MDSLAARHLERKTITYAEVCGKGASQIGFNEVAIERATEYAAEDAEVTLALHHAMWPQVE 60
           MDSLAARHLERKTITYAEVCGKGASQIGFNEVAIERATEYAAEDAEVTLALH AMWPQ+E
Sbjct: 450 MDSLAARHLERKTITYAEVCGKGASQIGFNEVAIERATEYAAEDAEVTLALHQAMWPQIE 509

Query: 61  HDDKLRFIYEKIEVPTSVVLQKIERNGVLIDSERLGQQSHDLGKRMLEIEQQAYDLAGQP 120
           HDDKLRFIYEKIEVPTSVVLQKIERNGVLIDSERLGQQSHDLGKRMLEIEQQAYDLAGQP
Sbjct: 510 HDDKLRFIYEKIEVPTSVVLQKIERNGVLIDSERLGQQSHDLGKRMLEIEQQAYDLAGQP 569

Query: 121 FNLNSPKQLGEILFGKLELPVVKKTASGAPSTDEEVLQKLAEDYPLPKVLLDYRGLAKLK 180
           FNLNSPKQLGEILFGKLELPVVKKTASGAPSTDEEVLQKLAEDYPLPKVLLDYRGLAKLK
Sbjct: 570 FNLNSPKQLGEILFGKLELPVVKKTASGAPSTDEEVLQKLAEDYPLPKVLLDYRGLAKLK 629

Query: 181 STYTDKLPKMINPASGRVHTNYAQAVAVTGRLSSNEPNLQNIPIRTPEGRRIREAFVAPE 240
           STYTDKLPKM+NPA+GRVHTNYAQAVAVTGRLSSN+PNLQNIPIRT EGRRIREAFVAPE
Sbjct: 630 STYTDKLPKMVNPATGRVHTNYAQAVAVTGRLSSNDPNLQNIPIRTAEGRRIREAFVAPE 689

Query: 241 GCVIVSADYSQIELRIMAHISEDENMLKAFANNEDIHKATAAEIFGIAPEQVESEQRRYA 300
           G VIVSADYSQIELRIMAHISEDENMLKAFANNEDIH+ATAAEIFGIAPEQVESEQRRYA
Sbjct: 690 GSVIVSADYSQIELRIMAHISEDENMLKAFANNEDIHRATAAEIFGIAPEQVESEQRRYA 749

Query: 301 KVINFGLIYGMSAFGLAGNLGIERSAAQMYIDKYFMRFSGVKRYMDETRLQAKARGYVET 360
           KVINFGLIYGMSAFGLA NLGIER+AAQMYIDKYFMRFSGVKRYMDETRLQAKARGYVET
Sbjct: 750 KVINFGLIYGMSAFGLASNLGIERAAAQMYIDKYFMRFSGVKRYMDETRLQAKARGYVET 809

Query: 361 VFGRRLWLPEINSPNGPRRQGAERAAINAPMQGTAADLIKLAMIAVQDWLESTGMKSRMI 420
           VFGRRLWLPEINSPNGPRRQGAERAAINAPMQGTAADLIK+AMIAVQDWLE+  +++RMI
Sbjct: 810 VFGRRLWLPEINSPNGPRRQGAERAAINAPMQGTAADLIKMAMIAVQDWLETNSLQTRMI 869

Query: 421 MQVHDELVLEVPQDELAVVREKLPELMKNVAELKVPLLAEVGIGKNWDEAH 471
           MQVHDELVLEVPQ EL +VREKLPELMKNVAELKVPLLAEVGIGKNWDEAH
Sbjct: 870 MQVHDELVLEVPQQELEMVREKLPELMKNVAELKVPLLAEVGIGKNWDEAH 920


  Database: BlastDatabases/689/689
    Posted date:  Apr 10, 2011 12:15 AM
  Number of letters in database: 1,619,870
  Number of sequences in database:  4735
  
Lambda     K      H
   0.317    0.133    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 4735
Number of Hits to DB: 1,416,788
Number of extensions: 58885
Number of successful extensions: 173
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 173
Number of HSP's successfully gapped: 1
Length of query: 471
Length of database: 1,619,870
Length adjustment: 89
Effective length of query: 382
Effective length of database: 1,198,455
Effective search space: 457809810
Effective search space used: 457809810
Neighboring words threshold: 11
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: 132 (55.5 bits)