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= 0059.0001.p
         (82 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300310170|ref|YP_003774262.1| diguanylate cyclase/phosphodies...   114   1e-27
gi|300311871|ref|YP_003775963.1| EAL domain-containing protein [...    79   5e-17
gi|300314042|ref|YP_003778134.1| signal transduction protein con...    77   2e-16
gi|300311036|ref|YP_003775128.1| signal transduction protein [He...    77   3e-16
gi|300312904|ref|YP_003776996.1| diguanylate cyclase/phosphodies...    75   7e-16

>gi|300310170|ref|YP_003774262.1| diguanylate
           cyclase/phosphodiesterase A protein [Herbaspirillum
           seropedicae SmR1]
          Length = 1002

 Score =  114 bits (286), Expect = 1e-27,   Method: Compositional matrix adjust.
 Identities = 57/73 (78%), Positives = 63/73 (86%)

Query: 1   LPNRSLLLVNANHAIANAARTKIPMAVLFIDLDRFKQINDSLGHQAGDELLRTVASRLQV 60
           LPNRSLLLV A  AIA A R    +AV+FIDLDRFKQ+NDSLGHQAGDELLRTVA+RLQ 
Sbjct: 566 LPNRSLLLVQAGQAIAAAERNCSTVAVMFIDLDRFKQVNDSLGHQAGDELLRTVATRLQS 625

Query: 61  EARKSDIVGRLSG 73
           +AR+SDIVGRLSG
Sbjct: 626 QARRSDIVGRLSG 638


>gi|300311871|ref|YP_003775963.1| EAL domain-containing protein
           [Herbaspirillum seropedicae SmR1]
          Length = 1036

 Score = 79.3 bits (194), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 50/73 (68%)

Query: 1   LPNRSLLLVNANHAIANAARTKIPMAVLFIDLDRFKQINDSLGHQAGDELLRTVASRLQV 60
           LPNR+LLL     AIA + RTK   A+LFIDLD FK +ND++GH+ GD LL+ VA RL  
Sbjct: 607 LPNRTLLLDRLKQAIALSLRTKTCAALLFIDLDHFKTLNDTIGHEKGDTLLKQVAQRLLA 666

Query: 61  EARKSDIVGRLSG 73
             R++D V R+ G
Sbjct: 667 NVRENDTVARVGG 679


>gi|300314042|ref|YP_003778134.1| signal transduction protein
           containing a membrane domain, an EAL and a GGDEF
           domain-containing protein [Herbaspirillum seropedicae
           SmR1]
          Length = 948

 Score = 77.4 bits (189), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 50/73 (68%)

Query: 1   LPNRSLLLVNANHAIANAARTKIPMAVLFIDLDRFKQINDSLGHQAGDELLRTVASRLQV 60
           L NR +L  +   AI  A R K  + V+F+DLDRFK +ND+LGH+AGD LLRTVA RL+ 
Sbjct: 527 LINRHMLRHHLEQAIGVAERQKQALWVVFVDLDRFKFVNDTLGHKAGDTLLRTVAGRLRA 586

Query: 61  EARKSDIVGRLSG 73
             R++D V RL G
Sbjct: 587 AVREADTVARLGG 599


>gi|300311036|ref|YP_003775128.1| signal transduction protein
           [Herbaspirillum seropedicae SmR1]
          Length = 750

 Score = 77.0 bits (188), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/73 (50%), Positives = 49/73 (67%)

Query: 1   LPNRSLLLVNANHAIANAARTKIPMAVLFIDLDRFKQINDSLGHQAGDELLRTVASRLQV 60
           LPNR LL       +A+A +   P+AV+FIDLDRFK +NDSLGH  GD+LL   A R++ 
Sbjct: 321 LPNRRLLGDMLQREVASAKKHAYPLAVVFIDLDRFKDVNDSLGHSVGDQLLVVAAQRVRA 380

Query: 61  EARKSDIVGRLSG 73
             R+ D+V RL+G
Sbjct: 381 SVREHDLVARLAG 393


>gi|300312904|ref|YP_003776996.1| diguanylate
           cyclase/phosphodiesterase with PAS/PAC sensor domains
           protein [Herbaspirillum seropedicae SmR1]
          Length = 701

 Score = 75.5 bits (184), Expect = 7e-16,   Method: Compositional matrix adjust.
 Identities = 39/73 (53%), Positives = 50/73 (68%)

Query: 1   LPNRSLLLVNANHAIANAARTKIPMAVLFIDLDRFKQINDSLGHQAGDELLRTVASRLQV 60
           LPNR++L  +   A+  A +     AV F+DLD+FK INDSLGHQ GDELL+TVA RLQ 
Sbjct: 274 LPNRNMLHEHLQRALRVARQKGALTAVAFVDLDQFKFINDSLGHQVGDELLKTVAQRLQA 333

Query: 61  EARKSDIVGRLSG 73
             R++D+V R  G
Sbjct: 334 CLREADMVARQGG 346


  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
   0.319    0.133    0.361 

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: 238,983
Number of extensions: 7512
Number of successful extensions: 60
Number of sequences better than 1.0e-08: 22
Number of HSP's gapped: 60
Number of HSP's successfully gapped: 22
Length of query: 82
Length of database: 1,619,870
Length adjustment: 53
Effective length of query: 29
Effective length of database: 1,368,915
Effective search space: 39698535
Effective search space used: 39698535
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 (21.8 bits)
S2: 123 (52.0 bits)