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= 0001.2522.p
         (336 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300311587|ref|YP_003775679.1| nuclease subunit of the excinuc...   518   e-148
gi|300311266|ref|YP_003775358.1| excinuclease ABC subunit C [Her...    55   6e-09

>gi|300311587|ref|YP_003775679.1| nuclease subunit of the
           excinuclease complex protein [Herbaspirillum seropedicae
           SmR1]
          Length = 317

 Score =  518 bits (1333), Expect = e-148,   Method: Compositional matrix adjust.
 Identities = 254/300 (84%), Positives = 270/300 (90%)

Query: 35  PAGLPLATFNAPQPAAHRAATFSYPLHIDRASIDALPAACGVYILRGVDDVPLYVGRSVN 94
           P GLPLATFNAPQPAAHRAATFSYPLHIDRASI+ALP+ACGVYILRG  D  LYVGRSVN
Sbjct: 16  PRGLPLATFNAPQPAAHRAATFSYPLHIDRASIEALPSACGVYILRGEGDQALYVGRSVN 75

Query: 95  LRSRVLAQLHHHEDQFLIARTRRIECRRTAGELGAALLENCLLRDLRPAHNKKPRSKRGL 154
           LRSRVLA LHH EDQFLI RTRRIEC RTAGELGAALLEN LLRDLRPAHNKK R+KRGL
Sbjct: 76  LRSRVLAHLHHAEDQFLIGRTRRIECLRTAGELGAALLENSLLRDLRPAHNKKQRAKRGL 135

Query: 155 FTLRISPQGQPLVAELTERESSRAENLFGLYTSQRAAQEALHKLVERHCLCSIVTGLEQA 214
           FTLR+  QGQPLVA++ + E +RA  LFGLYTS+RAAQEALHKLVE H LCSI TGLEQ 
Sbjct: 136 FTLRLDEQGQPLVAQVADHEFNRAGKLFGLYTSERAAQEALHKLVEHHGLCSIATGLEQG 195

Query: 215 SSPGMACFGRQIRRCRGACTGEESHEQHQQRLLQALQDLRILPWPYAGPMALVEQGDGWQ 274
             PGMACFGRQIRRCRGACTGEESHEQHQ RLLQAL+DLRILPWPYAGPM +VEQGDGWQ
Sbjct: 196 EGPGMACFGRQIRRCRGACTGEESHEQHQSRLLQALEDLRILPWPYAGPMGIVEQGDGWQ 255

Query: 275 QVHVIDHWRYLGSLDRDNRQLASRPAASLKGFDLESYKLVIQPYLLGQLELRPLPGLPLA 334
           Q+HVID WRYLGSLDR  R+L +RPAASLKGFDL++YKLVIQPYLLGQLELRPLPGLPLA
Sbjct: 256 QIHVIDQWRYLGSLDRQQRRLPARPAASLKGFDLDTYKLVIQPYLLGQLELRPLPGLPLA 315


>gi|300311266|ref|YP_003775358.1| excinuclease ABC subunit C
           [Herbaspirillum seropedicae SmR1]
          Length = 621

 Score = 55.5 bits (132), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 54/197 (27%), Positives = 84/197 (42%), Gaps = 15/197 (7%)

Query: 66  SIDALPAACGVYILRGVDDVPLYVGRSVNLRSRVLAQLHHHEDQ----FLIARTRRIECR 121
           ++  LP   GVY     +D  LYVG++ +L+ RV +             ++ R  R+E  
Sbjct: 19  TVARLPHLPGVYRYFDAEDNVLYVGKARDLKKRVSSYFQKTLTSPRIAMMVERIARLETT 78

Query: 122 RTAGELGAALLENCLLRDLRPAHNKKPRSKRGLFTLRISPQGQPLVAELTERESSRAENL 181
            T  E  A LLEN L++ LRP  N   R  +    L+I+    P +A        R +  
Sbjct: 79  VTRSEAEALLLENNLIKTLRPRFNILFRDDKSYPYLKITGHAFPRMAYYRGAVDKRNQ-Y 137

Query: 182 FGLYTSQRAAQEALHKLVE----RHCLCSIVTGLEQASSPGMACFGRQIRRCRGACTGEE 237
           FG + +  A +E++  L +    R C  ++       S+    C   QI RC G C    
Sbjct: 138 FGPFPNAGAVKESIQILQKVFLLRTCEDTVF------SNRTRPCLLHQIHRCSGPCVNLV 191

Query: 238 SHEQHQQRLLQALQDLR 254
           S E +   +  A + LR
Sbjct: 192 SREDYAIDVENASKFLR 208


  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
   0.322    0.137    0.417 

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: 1,027,789
Number of extensions: 41680
Number of successful extensions: 117
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 2
Length of query: 336
Length of database: 1,619,870
Length adjustment: 86
Effective length of query: 250
Effective length of database: 1,212,660
Effective search space: 303165000
Effective search space used: 303165000
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)