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= 0004.0009.p
         (598 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310202|ref|YP_003774294.1| DNA primase [Herbaspirillum ser...  1221   0.0  

>gi|300310202|ref|YP_003774294.1| DNA primase [Herbaspirillum
           seropedicae SmR1]
          Length = 598

 Score = 1221 bits (3158), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 597/598 (99%), Positives = 598/598 (100%)

Query: 1   VIPQSFIQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFG 60
           +IPQSFIQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFG
Sbjct: 1   MIPQSFIQDLLNRVDIVDVVGRYVQLKKGGANFMGLCPFHNEKSPSFTVSPTKQFYHCFG 60

Query: 61  CGAHGTAISFLIEYSGMGFVEAVKDLAQNVGMVVPEREDSIPLAQRQEKQAKSMALSDVM 120
           CGAHGTAISFLIEYSGMGFVEAVKDLAQNVGMVVPEREDSIPLAQRQEKQAKSMALSDVM
Sbjct: 61  CGAHGTAISFLIEYSGMGFVEAVKDLAQNVGMVVPEREDSIPLAQRQEKQAKSMALSDVM 120

Query: 121 TRANDFYRHQLRSAQPAIAYLKGRGLTGEIAARFGLGYSPDEWDSLRQVFPDYDNEALVE 180
           TRANDFYRHQLRSAQPAIAYLKGRGLTGEIAARFGLGYSPDEWDSLRQVFPDYDNEALVE
Sbjct: 121 TRANDFYRHQLRSAQPAIAYLKGRGLTGEIAARFGLGYSPDEWDSLRQVFPDYDNEALVE 180

Query: 181 SGLVIDKSEEGGAHRKRYDRFRGRIMFPIRNTKGQVIGFGGRVMDGGEPKYLNSPETPLF 240
           SGLVIDKSEEGGAHRKRYDRFRGRIMFPIRNTKGQVIGFGGRVMDGGEPKYLNSPETPLF
Sbjct: 181 SGLVIDKSEEGGAHRKRYDRFRGRIMFPIRNTKGQVIGFGGRVMDGGEPKYLNSPETPLF 240

Query: 241 QKGSELYGLFEARQAIREAGYALVTEGYMDVVALAQLGFPQAVATLGTACTPIHVQKLVR 300
           QKGSELYGLFEARQAIREAGYALVTEGYMDVVALAQLGFPQAVATLGTACTPIHVQKLVR
Sbjct: 241 QKGSELYGLFEARQAIREAGYALVTEGYMDVVALAQLGFPQAVATLGTACTPIHVQKLVR 300

Query: 301 QTDQVIFSFDGDNAGRRAARRALEACLPHASDNKTIKFLFLPKEHDPDSYVREMGAPAFE 360
           QTDQVIFSFDGDNAGRRAARRALEACLPHASDNKTIKFLFLPKEHDPDSYVREMGAPAFE
Sbjct: 301 QTDQVIFSFDGDNAGRRAARRALEACLPHASDNKTIKFLFLPKEHDPDSYVREMGAPAFE 360

Query: 361 EQIREALPLSQFLLREIIGENDLRTPEGRAHAQFAAKPLLQALPASALRLQIVRSVAQAT 420
           EQIREALPLSQFLLREIIGENDLRTPEGRAHAQFAAKPLLQALPASALRLQIVRSVAQAT
Sbjct: 361 EQIREALPLSQFLLREIIGENDLRTPEGRAHAQFAAKPLLQALPASALRLQIVRSVAQAT 420

Query: 421 QSTPAELEVLFELEKPVARVRAAPARSKRTAPVGLERQIMRLLVAHPQLAADLDAGALEA 480
           QSTPAELEVLFELEKPVARVRAAPARSKRTAPVGLERQIMRLLVAHPQLAADLDAGALEA
Sbjct: 421 QSTPAELEVLFELEKPVARVRAAPARSKRTAPVGLERQIMRLLVAHPQLAADLDAGALEA 480

Query: 481 IARIAPDQAEMLTHLVGVAQGMGEQANFAALVEHLREGGPEFDSMIAEIAAESESEFDVV 540
           IARIAPDQAEMLTHLVGVAQGMGEQANFAALVEHLREGGPEFDSMIAEIAAESESEFDVV
Sbjct: 481 IARIAPDQAEMLTHLVGVAQGMGEQANFAALVEHLREGGPEFDSMIAEIAAESESEFDVV 540

Query: 541 RAEMGGAIRQARIRALDEEMQMLVTSNLRTEEDRNRYRELMQRKEWLKRQAGAAVAAG 598
           RAEMGGAIRQARIRALDEEMQMLVTSNLRTEEDRNRYRELMQRKEWLKRQAGAAVAAG
Sbjct: 541 RAEMGGAIRQARIRALDEEMQMLVTSNLRTEEDRNRYRELMQRKEWLKRQAGAAVAAG 598


  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
   0.320    0.135    0.388 

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: 1,783,239
Number of extensions: 73673
Number of successful extensions: 251
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 1
Length of query: 598
Length of database: 1,619,870
Length adjustment: 91
Effective length of query: 507
Effective length of database: 1,188,985
Effective search space: 602815395
Effective search space used: 602815395
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 133 (55.8 bits)