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= 0001.1773.p
         (434 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311231|ref|YP_003775323.1| recombination factor RarA prote...   864   0.0  
gi|300309763|ref|YP_003773855.1| Holliday junction resolvase DNA...    60   4e-10
gi|300312975|ref|YP_003777067.1| DNA polymerase III subunit gamm...    59   9e-10

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

 Score =  864 bits (2233), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 420/433 (96%), Positives = 427/433 (98%)

Query: 1   MADLFAQEPAAPLAEALRPKTLDEVIGQSHLLGEGKPLRLAFQSGKPHSMIFWGPPGVGK 60
           MADLFAQEPAAPLAEALRPKTLDEVIGQSHLLGEGKPLRLAFQSGKPHSMIFWGPPGVGK
Sbjct: 1   MADLFAQEPAAPLAEALRPKTLDEVIGQSHLLGEGKPLRLAFQSGKPHSMIFWGPPGVGK 60

Query: 61  TTLARLTATAFQCEFIALSAVFSGVKDIRAAMEQAEQNLSMGKHTILFVDEIHRFNKSQQ 120
           TTLARLTATAF+CEFIALSAVFSGVKDIRAAMEQAEQNL+MGKHTILFVDEIHRFNKSQQ
Sbjct: 61  TTLARLTATAFECEFIALSAVFSGVKDIRAAMEQAEQNLAMGKHTILFVDEIHRFNKSQQ 120

Query: 121 DALLPYAESGLVTFIGATTENPSFEVNSALLSRAQVYVLKSLTDDELKLLLKRAQEKALG 180
           DALLPYAESGLVTFIGATTENPSFEVNSALLSRAQVYVLKSLTD+ELK LLKRAQ+KALG
Sbjct: 121 DALLPYAESGLVTFIGATTENPSFEVNSALLSRAQVYVLKSLTDEELKQLLKRAQDKALG 180

Query: 181 ELQFDAQATDTIIGYADGDARRFLNLLEQTETAARTTGTTLVTAEFLQNALTLNSRRFDK 240
           +LQFD QATDTIIGYADGDARRFLNLLEQT+TAARTTGT LVTAEFLQNALTLNSRRFDK
Sbjct: 181 DLQFDQQATDTIIGYADGDARRFLNLLEQTDTAARTTGTRLVTAEFLQNALTLNSRRFDK 240

Query: 241 GGDNFYDQISALHKSVRGSHPDAALYWLTRMLDGGADPRYLSRRIVRMAWEDIGLADPRA 300
           GGDNFYDQISALHKSVRGSHPDAALYWLTRMLDGGADPRYLSRRIVRMAWEDIGLADPRA
Sbjct: 241 GGDNFYDQISALHKSVRGSHPDAALYWLTRMLDGGADPRYLSRRIVRMAWEDIGLADPRA 300

Query: 301 MQIANDAALTYERLGSPEGELALGQAVIYLAVAAKSNAGYNAYNAARAFVKQDKSREVPV 360
           MQIANDAALTYERLGSPEGELALGQAVIYLAVAAKSNAGYNAYNAARAFVKQDKSREVPV
Sbjct: 301 MQIANDAALTYERLGSPEGELALGQAVIYLAVAAKSNAGYNAYNAARAFVKQDKSREVPV 360

Query: 361 HLRNAPTKLMKELGYGHEYRYAHDEPNAYAAGETYLPEGIAEPGWYQPVPRGLEIKIGEK 420
           HLRNAPTKLMKELGYGHEYRYAHDEPNAYAAGETYLP+GI EPGWYQPVPRGLEIKIGEK
Sbjct: 361 HLRNAPTKLMKELGYGHEYRYAHDEPNAYAAGETYLPDGIEEPGWYQPVPRGLEIKIGEK 420

Query: 421 LATLRQWDEEVGK 433
           LATLRQWDEE  K
Sbjct: 421 LATLRQWDEEARK 433


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

 Score = 60.1 bits (144), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 41/120 (34%), Positives = 62/120 (51%), Gaps = 11/120 (9%)

Query: 13  LAEALRPKTLDEVIGQSHLLGEGKP-LRLAFQSGKP--HSMIFWGPPGVGKTTLARLTAT 69
           +  ALRPK LDE +GQ  +  + +  +  A + G+P  H+++F GPPG+GKTT+A + A 
Sbjct: 26  IERALRPKQLDEYVGQEKVRAQLEIFISAARKRGEPLDHTLLF-GPPGLGKTTMAHIIAR 84

Query: 70  AFQCEFIALSA-VFSGVKDIRAAMEQAEQNLSMGKHTILFVDEIHRFNKSQQDALLPYAE 128
                    S  V     D+ A +   E N       +LF+DEIHR +   ++ L P  E
Sbjct: 85  EMGVNLRQTSGPVLERAGDLAALLTNLEAN------DVLFIDEIHRMSPVVEEILYPALE 138


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

 Score = 58.5 bits (140), Expect = 9e-10,   Method: Compositional matrix adjust.
 Identities = 59/230 (25%), Positives = 98/230 (42%), Gaps = 40/230 (17%)

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

Query: 72  QC-----------------------------EFIALSAVFS-GVKDIRAAMEQAEQNLSM 101
            C                             ++I + A  + GV ++   +EQA    S 
Sbjct: 63  NCVGPDGAGGITAAPCGVCEACVAIDAGRFVDYIEMDAASNRGVDEMAQLLEQAIYAPSN 122

Query: 102 GKHTILFVDEIHRFNKSQQDALLPYAESG--LVTFIGATTENPSFEVNSALLSRAQVYVL 159
            +  +  +DE+H       +A+L   E     + FI ATT+     V   +LSR   + L
Sbjct: 123 ARFKVYMIDEVHMLTNHAFNAMLKTLEEPPEHIKFILATTDPQKIPVT--VLSRCLQFNL 180

Query: 160 KSLTDDELKLLLKRAQEKALGELQFDAQATDTIIGYADGDARRFLNLLEQ 209
           K +    +   L     +    ++FDA A   +   A G  R  L+L +Q
Sbjct: 181 KQMPPGHIIGHLDNILNQE--GIEFDAPALRLLAQGASGSMRDALSLTDQ 228


  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    0.385 

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: 1,245,022
Number of extensions: 49768
Number of successful extensions: 255
Number of sequences better than 1.0e-08: 3
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 3
Length of query: 434
Length of database: 1,619,870
Length adjustment: 88
Effective length of query: 346
Effective length of database: 1,203,190
Effective search space: 416303740
Effective search space used: 416303740
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 (21.7 bits)
S2: 132 (55.5 bits)