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= 0030.0075.p
         (407 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...   704   0.0  
gi|300311912|ref|YP_003776004.1| DNA polymerase III subunit delt...    68   1e-12
gi|300311231|ref|YP_003775323.1| recombination factor RarA prote...    57   4e-09

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

 Score =  704 bits (1817), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 339/370 (91%), Positives = 352/370 (95%)

Query: 1   MSYQVLARKYRPRSFDTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK 60
           MSYQVLARKYRPRSFDTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK
Sbjct: 1   MSYQVLARKYRPRSFDTLVGQEHVVRALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAK 60

Query: 61  SLNCQGPDGNGGITAQPCGVCDACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAVYAP 120
           SLNC GPDG GGITA PCGVC+ACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQA+YAP
Sbjct: 61  SLNCVGPDGAGGITAAPCGVCEACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAIYAP 120

Query: 121 SNARFKVYMIDEVHMLTNHAFNSMLKTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNL 180
           SNARFKVYMIDEVHMLTNHAFN+MLKTLEEPPEH+KFILATTDPQKIPVTVLSRCLQFNL
Sbjct: 121 SNARFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHIKFILATTDPQKIPVTVLSRCLQFNL 180

Query: 181 KQMPPGHIISHLDNILGQENIEFEAPALRLLAQGAHGSMRDALSLTDQAIAYAAGKVTLE 240
           KQMPPGHII HLDNIL QE IEF+APALRLLAQGA GSMRDALSLTDQAIAYAAGKVTLE
Sbjct: 181 KQMPPGHIIGHLDNILNQEGIEFDAPALRLLAQGASGSMRDALSLTDQAIAYAAGKVTLE 240

Query: 241 AVQGMLGALDQSYLIRVLDALAAQDGSGLLAVADEMATRSLSYNAALQDLATLLHQIALA 300
           AVQGMLGALDQSYLIR+LDALA QDG+ LL VAD+MATRSLSYNAALQDL TLLHQIALA
Sbjct: 241 AVQGMLGALDQSYLIRILDALAVQDGAALLGVADDMATRSLSYNAALQDLGTLLHQIALA 300

Query: 301 QTVPAALAEDLPQREDIVRLASQFSAEEAQLFYQIVVHGRNELGLAPDEYAGFSMTLLRM 360
           Q VPAALA+DLP REDI+RL+ QFS E  QLFYQI VHGRNELGLAPDEYAGFSMTLLRM
Sbjct: 301 QAVPAALADDLPNREDILRLSGQFSPEHVQLFYQIAVHGRNELGLAPDEYAGFSMTLLRM 360

Query: 361 LAFRPVAANA 370
           LAFRPV+A+A
Sbjct: 361 LAFRPVSASA 370


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

 Score = 68.2 bits (165), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 56/180 (31%), Positives = 74/180 (41%), Gaps = 33/180 (18%)

Query: 34  QQRLHHAYLFTGTRGVGKTTLSRILAKSLNCQGPDGNGGITAQPCGVCDACVAIDAGRFV 93
           ++RL HA LF G  G GKT      AKSL C+ P       A  CGVC +C         
Sbjct: 24  RERLPHALLFYGAAGTGKTQFVEAFAKSLLCESPTPE----AHACGVCASCNWFSQSNHP 79

Query: 94  DY--IEMDAASNRGVDEMAQLLEQAVYAPSNARFKVYMIDEVHMLTNHAFNS-------- 143
           DY  +  +   +   D+ A   E+     S A  K   ID++  L +    S        
Sbjct: 80  DYRRVRPEVLDDETADDEAGE-EKKTAKASKAPSKDIKIDQIRALADFMNVSTHRSGLRV 138

Query: 144 -ML---------------KTLEEPPEHVKFILATTDPQKIPVTVLSRCLQFNLKQMPPGH 187
            ML               KTLEEPP    F+L +    ++  T+LSRC +F L    PGH
Sbjct: 139 VMLYPAEALNTAAANALLKTLEEPPPGTMFLLLSNRLDRLLPTILSRCRKFALSA--PGH 196


>gi|300311231|ref|YP_003775323.1| recombination factor RarA protein
           [Herbaspirillum seropedicae SmR1]
          Length = 434

 Score = 56.6 bits (135), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 59/232 (25%), Positives = 100/232 (43%), Gaps = 44/232 (18%)

Query: 6   LARKYRPRSFDTLVGQEHVV---RALTHALEQQRLHHAYLFTGTRGVGKTTLSRILAKSL 62
           LA   RP++ D ++GQ H++   + L  A +  +  H+ +F G  GVGKTTL+R+ A + 
Sbjct: 13  LAEALRPKTLDEVIGQSHLLGEGKPLRLAFQSGK-PHSMIFWGPPGVGKTTLARLTATAF 71

Query: 63  NCQGPDGNGGITAQPCGVCDACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAVYAPSN 122
            C+                             +I + A  + GV ++   +EQA    + 
Sbjct: 72  ECE-----------------------------FIALSAVFS-GVKDIRAAMEQAEQNLAM 101

Query: 123 ARFKVYMIDEVHMLTNHAFNSMLKTLEEPPEHVKFILATTDPQKIPVT--VLSRCLQFNL 180
            +  +  +DE+H       +++L   E     V FI ATT+     V   +LSR   + L
Sbjct: 102 GKHTILFVDEIHRFNKSQQDALLPYAES--GLVTFIGATTENPSFEVNSALLSRAQVYVL 159

Query: 181 KQMPPGHIISHL----DNILGQENIEFEAPALRLLAQGAHGSMRDALSLTDQ 228
           K +    +   L    D  LG  +++F+  A   +   A G  R  L+L +Q
Sbjct: 160 KSLTDEELKQLLKRAQDKALG--DLQFDQQATDTIIGYADGDARRFLNLLEQ 209


  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    0.133    0.382 

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: 1,118,865
Number of extensions: 45967
Number of successful extensions: 240
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 238
Number of HSP's successfully gapped: 3
Length of query: 407
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 320
Effective length of database: 1,207,925
Effective search space: 386536000
Effective search space used: 386536000
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: 132 (55.5 bits)