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= 0027.0001.p
         (370 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...   635   0.0  
gi|300311266|ref|YP_003775358.1| excinuclease ABC subunit C [Her...    55   7e-09

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

 Score =  635 bits (1639), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 313/317 (98%), Positives = 315/317 (99%)

Query: 54  VQEGEHGLPALPSLPPRGLPLATFNAPQPAAHRAATFSYPLHIDRASIEALPSACGVYIL 113
           +QEGEHGLPALPS PPRGLPLATFNAPQPAAHRAATFSYPLHIDRASIEALPSACGVYIL
Sbjct: 1   MQEGEHGLPALPSFPPRGLPLATFNAPQPAAHRAATFSYPLHIDRASIEALPSACGVYIL 60

Query: 114 RGEGDQALYVGRSVNLRSRVLAHLHHAEDQFLIGRTRRIECLRTAGELGAALLENSLLRD 173
           RGEGDQALYVGRSVNLRSRVLAHLHHAEDQFLIGRTRRIECLRTAGELGAALLENSLLRD
Sbjct: 61  RGEGDQALYVGRSVNLRSRVLAHLHHAEDQFLIGRTRRIECLRTAGELGAALLENSLLRD 120

Query: 174 LRPAHNKKQRAKRSLFTLRLDEQGQPLVAQVADHEFNRAGKLFGLYTSERAAQEALHKLV 233
           LRPAHNKKQRAKR LFTLRLDEQGQPLVAQVADHEFNRAGKLFGLYTSERAAQEALHKLV
Sbjct: 121 LRPAHNKKQRAKRGLFTLRLDEQGQPLVAQVADHEFNRAGKLFGLYTSERAAQEALHKLV 180

Query: 234 EHHGLCSIATGLEQGEGPGMACFGRQIRRCRGACTGEESHEQHQSRLLQALEDLRILPWP 293
           EHHGLCSIATGLEQGEGPGMACFGRQIRRCRGACTGEESHEQHQSRLLQALEDLRILPWP
Sbjct: 181 EHHGLCSIATGLEQGEGPGMACFGRQIRRCRGACTGEESHEQHQSRLLQALEDLRILPWP 240

Query: 294 YAGPMGIVEQGDGWQQIHVIDQWRYLGSLDRQQRRLPARPAASLKGFDLDTYKLVIQPYL 353
           YAGPMGIVEQGDGWQQIHVIDQWRYLGSLDRQQRRLPARPAASLKGFDLDTYKLVIQPYL
Sbjct: 241 YAGPMGIVEQGDGWQQIHVIDQWRYLGSLDRQQRRLPARPAASLKGFDLDTYKLVIQPYL 300

Query: 354 LGQLELRPLPGLPLAHP 370
           LGQLELRPLPGLPLA+P
Sbjct: 301 LGQLELRPLPGLPLAYP 317


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

 Score = 55.5 bits (132), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 55/205 (26%), Positives = 87/205 (42%), Gaps = 23/205 (11%)

Query: 100 SIEALPSACGVYILRGEGDQALYVGRSVNLRSRVLAHLHHAEDQ----FLIGRTRRIECL 155
           ++  LP   GVY      D  LYVG++ +L+ RV ++            ++ R  R+E  
Sbjct: 19  TVARLPHLPGVYRYFDAEDNVLYVGKARDLKKRVSSYFQKTLTSPRIAMMVERIARLETT 78

Query: 156 RTAGELGAALLENSLLRDLRPAHNKKQRAKRSLFTLRLDEQGQPLVAQVADHEFNRAGKL 215
            T  E  A LLEN+L++ LRP  N   R  +S   L++     P +A       ++  + 
Sbjct: 79  VTRSEAEALLLENNLIKTLRPRFNILFRDDKSYPYLKITGHAFPRMAYYRG-AVDKRNQY 137

Query: 216 FGLYTSERAAQEALHKLVEHHGLCSIA-TGLEQGEGPGMACFGRQIRRCRGACTGEESHE 274
           FG + +  A +E++  L +   L +   T       P   C   QI RC G C    S E
Sbjct: 138 FGPFPNAGAVKESIQILQKVFLLRTCEDTVFSNRTRP---CLLHQIHRCSGPCVNLVSRE 194

Query: 275 QH--------------QSRLLQALE 285
            +              QS +++ALE
Sbjct: 195 DYAIDVENASKFLRGRQSEVMEALE 219


  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
   0.321    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: 1,174,858
Number of extensions: 49307
Number of successful extensions: 152
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 150
Number of HSP's successfully gapped: 2
Length of query: 370
Length of database: 1,619,870
Length adjustment: 87
Effective length of query: 283
Effective length of database: 1,207,925
Effective search space: 341842775
Effective search space used: 341842775
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)