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= 0002.0262.p
         (298 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313251|ref|YP_003777343.1| excinuclease ATPase subunit [He...   479   e-137

>gi|300313251|ref|YP_003777343.1| excinuclease ATPase subunit
           [Herbaspirillum seropedicae SmR1]
          Length = 952

 Score =  479 bits (1234), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 236/253 (93%), Positives = 246/253 (97%)

Query: 45  APIGRTPRSNPATYTGLFTPIRDLFATVPAAKERGYSAGRFSFNVKGGRCEACQGDGVIK 104
           APIGRTPRSNPATYTGLFTPIRDLFATVP AKERGYSAGRFSFNVKGGRCEACQGDGVIK
Sbjct: 698 APIGRTPRSNPATYTGLFTPIRDLFATVPMAKERGYSAGRFSFNVKGGRCEACQGDGVIK 757

Query: 105 VEMHFLPDVYVPCDVCHGKRYNRETLEVQYKGKNITEILEMTVEDAHTFFLPVPLIARKL 164
           VEMHFLPDVYVPCDVCHGKRYNRETLEVQYKGKNITEIL+MTVEDAH FF PVPLIARKL
Sbjct: 758 VEMHFLPDVYVPCDVCHGKRYNRETLEVQYKGKNITEILDMTVEDAHEFFKPVPLIARKL 817

Query: 165 QTLLDVGLGYIKLGQSATTLSGGEAQRVKLSLELSKRDTGRTLYILDEPTTGLHFHDIDL 224
           QTLLDVGLGYIKLGQSATTLSGGEAQRVKLSLELSKRDTGRTLYILDEPTTGLHFHDIDL
Sbjct: 818 QTLLDVGLGYIKLGQSATTLSGGEAQRVKLSLELSKRDTGRTLYILDEPTTGLHFHDIDL 877

Query: 225 LLKVIHRLRDQGNTLAIIEHNLDVIKTADWVIDLGPEGGAGGGKIIAVGSPEDIARNPES 284
           LLKVIHRLRDQGNT+ IIEHNLDVIKTADW+IDLGPEGGAGGG+I+A G+PE++A+NP S
Sbjct: 878 LLKVIHRLRDQGNTVTIIEHNLDVIKTADWIIDLGPEGGAGGGRIVAAGTPEEVAKNPAS 937

Query: 285 ITGHYLAPLLKKK 297
           +TG YLAPLLKKK
Sbjct: 938 VTGKYLAPLLKKK 950



 Score =  127 bits (318), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 74/192 (38%), Positives = 108/192 (56%), Gaps = 19/192 (9%)

Query: 117 CDVCHGKRYNRETLEVQY----KGKNITEILEMTVEDAHTFFLPVPL------------- 159
           C  CHG R   E   V+     + + I E+    + +  +FF  + L             
Sbjct: 410 CPSCHGARLRVEARYVKVGSGKQQRAIYEVAATPLRETLSFFETLKLTGAKKEIADRIIK 469

Query: 160 -IARKLQTLLDVGLGYIKLGQSATTLSGGEAQRVKLSLELSKRDTGRTLYILDEPTTGLH 218
            I  +L  L +VGL Y+ L +SA TLSGGEAQR++L+ ++    TG  +Y+LDEP+ GLH
Sbjct: 470 EIVSRLTFLNNVGLDYLSLERSADTLSGGEAQRIRLASQIGSGLTG-VMYVLDEPSIGLH 528

Query: 219 FHDIDLLLKVIHRLRDQGNTLAIIEHNLDVIKTADWVIDLGPEGGAGGGKIIAVGSPEDI 278
             D D L+  +  LRD GNT+ ++EH+ D I+TAD+V+D+G   G  GG +IA G   DI
Sbjct: 529 QRDNDRLIDTLKHLRDIGNTVLVVEHDEDAIRTADYVVDMGIGAGVHGGDVIAHGPLPDI 588

Query: 279 ARNPESITGHYL 290
            +N +S+T  YL
Sbjct: 589 LKNKKSLTAKYL 600


  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
   0.318    0.136    0.403 

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: 759,594
Number of extensions: 29507
Number of successful extensions: 186
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 2
Length of query: 298
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 213
Effective length of database: 1,217,395
Effective search space: 259305135
Effective search space used: 259305135
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: 130 (54.7 bits)