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= 0002.0416.p
         (295 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF famil...    61   9e-11
gi|300312320|ref|YP_003776412.1| response regulator protein [Her...    59   6e-10
gi|300312976|ref|YP_003777068.1| GGDEF family protein [Herbaspir...    59   7e-10
gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane prot...    58   1e-09
gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767...    57   1e-09

>gi|300310067|ref|YP_003774159.1| diguanylate cyclase GGDEF family
           protein [Herbaspirillum seropedicae SmR1]
          Length = 369

 Score = 61.2 bits (147), Expect = 9e-11,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 39/67 (58%)

Query: 229 NAHLYEMATRDPLTGLANRRQFDEYSNREFRLARRTAKPLSMAVCDIDQFQQINDKHGRA 288
           N  L  ++  D LTG+ANRR FDE   +E+R + R   PL +A  D+D F+  ND +G  
Sbjct: 190 NEQLRSLSLTDGLTGIANRRSFDETLEQEWRRSMRHGTPLMLAFIDVDWFKPYNDHYGHL 249

Query: 289 VGDAXPR 295
            GDA  R
Sbjct: 250 AGDAVLR 256


>gi|300312320|ref|YP_003776412.1| response regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 341

 Score = 58.5 bits (140), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 29/67 (43%), Positives = 39/67 (58%)

Query: 229 NAHLYEMATRDPLTGLANRRQFDEYSNREFRLARRTAKPLSMAVCDIDQFQQINDKHGRA 288
           N  L  +   D LTG+ANRR FD+Y   E+R ARR    L++ + D+D F+  ND +G  
Sbjct: 167 NFELQRLTNTDGLTGIANRRYFDDYLGAEWRRARRDGLDLALLLIDVDFFKLYNDNYGHV 226

Query: 289 VGDAXPR 295
            GDA  R
Sbjct: 227 AGDAVLR 233


>gi|300312976|ref|YP_003777068.1| GGDEF family protein
           [Herbaspirillum seropedicae SmR1]
          Length = 324

 Score = 58.5 bits (140), Expect = 7e-10,   Method: Compositional matrix adjust.
 Identities = 29/58 (50%), Positives = 36/58 (62%)

Query: 235 MATRDPLTGLANRRQFDEYSNREFRLARRTAKPLSMAVCDIDQFQQINDKHGRAVGDA 292
           MAT D LTG++NRR FD  +      +RR   P  M   D+DQF+QIND+ G A GDA
Sbjct: 164 MATIDELTGISNRRGFDALARHALANSRRMDWPACMLYFDLDQFKQINDRFGHAEGDA 221


>gi|300310347|ref|YP_003774439.1| GGDEF domain transmembrane protein
           [Herbaspirillum seropedicae SmR1]
          Length = 334

 Score = 57.8 bits (138), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 29/69 (42%), Positives = 40/69 (57%)

Query: 224 KIRLYNAHLYEMATRDPLTGLANRRQFDEYSNREFRLARRTAKPLSMAVCDIDQFQQIND 283
           ++   N  L  +A  D LTGLANR + DE  + E   A R  K LS+ + DID F+++ND
Sbjct: 151 RVERLNEKLALLAVTDKLTGLANRMKLDEVLDNEINRADRYGKNLSLILLDIDHFKEVND 210

Query: 284 KHGRAVGDA 292
             G + GDA
Sbjct: 211 NFGHSTGDA 219


>gi|300312078|ref|YP_003776170.1| hypothetical protein Hsero_2767
           [Herbaspirillum seropedicae SmR1]
          Length = 534

 Score = 57.4 bits (137), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 28/61 (45%), Positives = 36/61 (59%)

Query: 231 HLYEMATRDPLTGLANRRQFDEYSNREFRLARRTAKPLSMAVCDIDQFQQINDKHGRAVG 290
            + E+   D LTG  NRR  DE  +RE   A R   PL +A+ D+D F++IND HG A G
Sbjct: 359 QMGELVREDQLTGSLNRRGMDESLDREITNALRRDTPLCVALLDLDDFKRINDTHGHATG 418

Query: 291 D 291
           D
Sbjct: 419 D 419


  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
   0.323    0.134    0.373 

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: 685,089
Number of extensions: 21738
Number of successful extensions: 124
Number of sequences better than 1.0e-08: 12
Number of HSP's gapped: 131
Number of HSP's successfully gapped: 12
Length of query: 295
Length of database: 1,619,870
Length adjustment: 85
Effective length of query: 210
Effective length of database: 1,217,395
Effective search space: 255652950
Effective search space used: 255652950
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 (22.0 bits)
S2: 130 (54.7 bits)