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= 0026.0041.p
         (272 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313028|ref|YP_003777120.1| two component response regulato...   125   4e-30
gi|300312425|ref|YP_003776517.1| nitrogen assimilation transcrip...    67   1e-12
gi|300313791|ref|YP_003777883.1| response regulator protein [Her...    59   4e-10
gi|300311805|ref|YP_003775897.1| two component hybrid sensor his...    57   1e-09

>gi|300313028|ref|YP_003777120.1| two component response regulator
           protein [Herbaspirillum seropedicae SmR1]
          Length = 448

 Score =  125 bits (314), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 60/159 (37%), Positives = 106/159 (66%)

Query: 11  PRTLLLVDDETNILSALKRLLRQDKYDIVTANNGQEALEALKSGPVDVIVTDQRMPGMTG 70
           P  +LLVDDE +ILSALKR  R   Y ++ A + + ALE + +  VD++++D RMPGM G
Sbjct: 22  PPCVLLVDDEQSILSALKRTFRPQGYRLIMATSAEAALEMMAASEVDLVISDMRMPGMNG 81

Query: 71  VEFLRLAKESYPDTVRIVLSGYTELQSVTDAVNEGAVYKFLTKPWDDGQLRGHVAEAFRR 130
            +FL   ++ +P T+RI+L+GY+E+ S   A+N+G +  +L+KPWDD +L   VA A   
Sbjct: 82  AQFLAKVRQQWPSTMRILLTGYSEIGSTISAINDGGINHYLSKPWDDRELLLIVAHALEE 141

Query: 131 KEMADENLRLQQQLQMANLALEETNKELDKLLKVQEERI 169
           +++  + + L+++++  NL L + N++L++ ++ + E +
Sbjct: 142 QQLRKQKMALERKVREQNLQLADFNRQLERQVQSRTEEL 180


>gi|300312425|ref|YP_003776517.1| nitrogen assimilation
           transcription activator protein [Herbaspirillum
           seropedicae SmR1]
          Length = 500

 Score = 67.4 bits (163), Expect = 1e-12,   Method: Compositional matrix adjust.
 Identities = 32/105 (30%), Positives = 65/105 (61%), Gaps = 1/105 (0%)

Query: 12  RTLLLVDDETNILSALKRLLRQDKYDIVTANNGQEALEALKSGPVDVIVTDQRMPGMTGV 71
           + + +VDD+ +I   L++ L ++     + ++ ++A+ AL++G   V+V+D RMPG +G+
Sbjct: 2   KPIWIVDDDESIRWVLEKALARENLATQSFSSARDAIAALQNGTPQVLVSDIRMPGASGL 61

Query: 72  EFLRLAKESYPDTVRIVLSGYTELQSVTDAVNEGAVYKFLTKPWD 116
           E L+  K  +P    I+++ +++L S   A   GA +++L KP+D
Sbjct: 62  ELLQTVKAKHPGIPVIIITAFSDLDSAVSAFQGGA-FEYLAKPFD 105


>gi|300313791|ref|YP_003777883.1| response regulator protein
           [Herbaspirillum seropedicae SmR1]
          Length = 206

 Score = 59.3 bits (142), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 40/121 (33%), Positives = 60/121 (49%), Gaps = 1/121 (0%)

Query: 12  RTLLLVDDETNILSALKRLLRQDKYDIVTANNGQEALEALKSGPVDVIVTDQRMPGMTGV 71
           RT+ +VDD+  + +AL RLL    Y      +  E L+A        ++ D +MPG  G 
Sbjct: 3   RTVFVVDDDNMVRTALLRLLASAGYAAHGFASADEFLQARLPAVPCCLLLDMKMPGSDGF 62

Query: 72  EFLRLAKESYPDTVRIVLSGYTELQSVTDAVNEGAVYKFLTKPWDDGQLRGHVAEAFRRK 131
           E +R  +        I +SGY  + +   A+  GA ++FLTKP  D +L G V EA +  
Sbjct: 63  EVVRRLERRGDAIPVIFISGYGTIPTTVQAMKAGA-HEFLTKPIQDERLLGAVEEALQIA 121

Query: 132 E 132
           E
Sbjct: 122 E 122


>gi|300311805|ref|YP_003775897.1| two component hybrid sensor
            histidine kinase/response regulator protein
            [Herbaspirillum seropedicae SmR1]
          Length = 1278

 Score = 57.4 bits (137), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 38/108 (35%), Positives = 55/108 (50%), Gaps = 4/108 (3%)

Query: 14   LLLVDDETNILSALKRLLRQDKYDIVTANNGQEALEALKSGPVDVIVTDQRMPGMTGVEF 73
            LL+V+D  +    +  LL    +      +G+EAL+AL+    DV+ TD  +PGM+GVE 
Sbjct: 1166 LLVVEDNIDSQQLVCELLETLGHQARGVISGEEALQALEEQGFDVLFTDVNLPGMSGVEL 1225

Query: 74   LRLAKESYPDTVRIVLSGYTELQSVTDAVNEGAVYKFLTKPWDDGQLR 121
             + A   +PD   I  SGY  +     A N G     L KP+D  QL+
Sbjct: 1226 AKAALGRFPDLAVIFASGYGTMV----ARNVGFAAHALPKPYDIDQLQ 1269


  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
   0.316    0.133    0.363 

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: 726,121
Number of extensions: 26557
Number of successful extensions: 191
Number of sequences better than 1.0e-08: 7
Number of HSP's gapped: 208
Number of HSP's successfully gapped: 7
Length of query: 272
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 188
Effective length of database: 1,222,130
Effective search space: 229760440
Effective search space used: 229760440
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 (21.6 bits)
S2: 130 (54.7 bits)