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= 0001.3590.p
         (394 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300312975|ref|YP_003777067.1| DNA polymerase III subunit gamm...   743   0.0  
gi|300311912|ref|YP_003776004.1| DNA polymerase III subunit delt...    65   1e-11

>gi|300312975|ref|YP_003777067.1| DNA polymerase III subunit
           gamma/tau [Herbaspirillum seropedicae SmR1]
          Length = 712

 Score =  743 bits (1919), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 374/412 (90%), Positives = 377/412 (91%), Gaps = 19/412 (4%)

Query: 1   MSYQVLARKYRPRSFDTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK 60
           MSYQVLARKYRPRSFDTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK
Sbjct: 1   MSYQVLARKYRPRSFDTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK 60

Query: 61  SLNCVGPDGTGGITAAPCGVCEACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAIYAP 120
           SLNCVGPDG GGITAAPCGVCEACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAIYAP
Sbjct: 61  SLNCVGPDGAGGITAAPCGVCEACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAIYAP 120

Query: 121 SNARFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHIKFILATTDPQKIPVTVLSRCLQFNL 180
           SNARFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHIKFILATTDPQKIPVTVLSRCLQFNL
Sbjct: 121 SNARFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHIKFILATTDPQKIPVTVLSRCLQFNL 180

Query: 181 KQMPPGHIISHLDNILHQEGIEFDPPALRLLAQGASGSMRDALSLTDQAIAYAAGKVTLE 240
           KQMPPGHII HLDNIL+QEGIEFD PALRLLAQGASGSMRDALSLTDQAIAYAAGKVTLE
Sbjct: 181 KQMPPGHIIGHLDNILNQEGIEFDAPALRLLAQGASGSMRDALSLTDQAIAYAAGKVTLE 240

Query: 241 AVQGMLGALDQSYLIRVLDALAVQDGAALLGVADDMATRSLSYNAALQDLGTLLHQIALA 300
           AVQGMLGALDQSYLIR+LDALAVQDGAALLGVADDMATRSLSYNAALQDLGTLLHQIALA
Sbjct: 241 AVQGMLGALDQSYLIRILDALAVQDGAALLGVADDMATRSLSYNAALQDLGTLLHQIALA 300

Query: 301 QAVPAALADDLPNREDILRLSAQFSAEHVQLFYQIVVHGRNELGLAPDEYAGFSMTLLRM 360
           QAVPAALADDLPNREDILRLS QFS EHVQLFYQI VHGRNELGLAPDEYAGFSMTLLRM
Sbjct: 301 QAVPAALADDLPNREDILRLSGQFSPEHVQLFYQIAVHGRNELGLAPDEYAGFSMTLLRM 360

Query: 361 LAFRPVSASA------------------TAPVPAAPV-APAAGATGATGPRT 393
           LAFRPVSASA                  TAP  AAP+ AP    T A   RT
Sbjct: 361 LAFRPVSASATAPIPAASSAPAAAGGRPTAPRQAAPLMAPQVAVTSAPVSRT 412


>gi|300311912|ref|YP_003776004.1| DNA polymerase III subunit delta
           [Herbaspirillum seropedicae SmR1]
          Length = 345

 Score = 64.7 bits (156), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 57/180 (31%), Positives = 75/180 (41%), Gaps = 33/180 (18%)

Query: 34  QQRLHHAYLFTGTRGVGKTTLSRILAKSLNCVGPDGTGGITAAPCGVCEACVAIDAGRFV 93
           ++RL HA LF G  G GKT      AKSL C  P       A  CGVC +C         
Sbjct: 24  RERLPHALLFYGAAGTGKTQFVEAFAKSLLCESPT----PEAHACGVCASCNWFSQSNHP 79

Query: 94  DY--IEMDAASNRGVDEMAQLLEQAIYAPSNARFKVYMIDEVHMLTNH------------ 139
           DY  +  +   +   D+ A   E+     S A  K   ID++  L +             
Sbjct: 80  DYRRVRPEVLDDETADDEAG-EEKKTAKASKAPSKDIKIDQIRALADFMNVSTHRSGLRV 138

Query: 140 ------------AFNAMLKTLEEPPEHIKFILATTDPQKIPVTVLSRCLQFNLKQMPPGH 187
                       A NA+LKTLEEPP    F+L +    ++  T+LSRC +F L    PGH
Sbjct: 139 VMLYPAEALNTAAANALLKTLEEPPPGTMFLLLSNRLDRLLPTILSRCRKFALSA--PGH 196


  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
   0.321    0.134    0.386 

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: 1,084,368
Number of extensions: 43324
Number of successful extensions: 220
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 2
Length of query: 394
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 307
Effective length of database: 1,207,925
Effective search space: 370832975
Effective search space used: 370832975
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 (21.9 bits)
S2: 131 (55.1 bits)