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= 0002.0040.p
         (351 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309763|ref|YP_003773855.1| Holliday junction resolvase DNA...   686   0.0  
gi|300311231|ref|YP_003775323.1| recombination factor RarA prote...    60   4e-10

>gi|300309763|ref|YP_003773855.1| Holliday junction resolvase DNA
           helicase subunit [Herbaspirillum seropedicae SmR1]
          Length = 351

 Score =  686 bits (1770), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 342/350 (97%), Positives = 348/350 (99%)

Query: 1   MSIQTDDFSEQRIISATPASANEEAVERALRPKQLDEYVGQEKVRSQLEIFISAARKRGE 60
           MSIQTDDFSEQRIISATPASANEEA+ERALRPKQLDEYVGQEKVR+QLEIFISAARKRGE
Sbjct: 1   MSIQTDDFSEQRIISATPASANEEAIERALRPKQLDEYVGQEKVRAQLEIFISAARKRGE 60

Query: 61  PLDHTLLFGPPGLGKTTMAHIIAREMGVNLRQTSGPVLERAGDLAALLTNLEANDVLFID 120
           PLDHTLLFGPPGLGKTTMAHIIAREMGVNLRQTSGPVLERAGDLAALLTNLEANDVLFID
Sbjct: 61  PLDHTLLFGPPGLGKTTMAHIIAREMGVNLRQTSGPVLERAGDLAALLTNLEANDVLFID 120

Query: 121 EIHRMSPVVEEILYPALEDYQIDIMIGEGPAARSVRLDLQPFTLVGATTRAGMLTNPLRD 180
           EIHRMSPVVEEILYPALEDYQIDIMIGEGPAARSVRLDLQPFTLVGATTRAGMLTNPLRD
Sbjct: 121 EIHRMSPVVEEILYPALEDYQIDIMIGEGPAARSVRLDLQPFTLVGATTRAGMLTNPLRD 180

Query: 181 RFGIVARLEFYTPPELARIVTRSAGLLNAPIVEEGALEIARRSRGTPRIANRLLRRVRDY 240
           RFGIVARLEFYTPPELARIVTRSAGLLNAPIVE+GALEIARRSRGTPRIANRLLRRVRDY
Sbjct: 181 RFGIVARLEFYTPPELARIVTRSAGLLNAPIVEDGALEIARRSRGTPRIANRLLRRVRDY 240

Query: 241 AEVKGEGRITREMADAALVMLDVDPVGFDLMDRKLLEAVLFKFGGGPVGLDNLAAAIGEE 300
           AEVKG+GRITREMADAALVMLDVDPVGFDLMDRKLLEAVLFKFGGGPVGLDNLAAAIGEE
Sbjct: 241 AEVKGQGRITREMADAALVMLDVDPVGFDLMDRKLLEAVLFKFGGGPVGLDNLAAAIGEE 300

Query: 301 RDTIEDVLEPYLIQQGYLQRTPRGRIATGLAYQHFGVTAPQTGPNGELWG 350
           RDTIEDVLEPYLIQQGYLQRTPRGRIATG AYQHFGVTAP+T PNG+LWG
Sbjct: 301 RDTIEDVLEPYLIQQGYLQRTPRGRIATGAAYQHFGVTAPRTSPNGDLWG 350


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

 Score = 59.7 bits (143), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 41/117 (35%), Positives = 61/117 (52%), Gaps = 11/117 (9%)

Query: 29  ALRPKQLDEYVGQEKVRSQLEIFISAARKRGEPLDHTLLF-GPPGLGKTTMAHIIAREMG 87
           ALRPK LDE +GQ  +  + +  +  A + G+P  H+++F GPPG+GKTT+A + A    
Sbjct: 16  ALRPKTLDEVIGQSHLLGEGKP-LRLAFQSGKP--HSMIFWGPPGVGKTTLARLTATAFE 72

Query: 88  VNLRQTSGPVLERAGDLAALLTNLEAN------DVLFIDEIHRMSPVVEEILYPALE 138
                 S  V     D+ A +   E N       +LF+DEIHR +   ++ L P  E
Sbjct: 73  CEFIALSA-VFSGVKDIRAAMEQAEQNLAMGKHTILFVDEIHRFNKSQQDALLPYAE 128


  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    0.138    0.393 

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: 1,166,965
Number of extensions: 52531
Number of successful extensions: 248
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 247
Number of HSP's successfully gapped: 2
Length of query: 351
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 265
Effective length of database: 1,212,660
Effective search space: 321354900
Effective search space used: 321354900
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: 131 (55.1 bits)