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= 0002.0096.p
         (237 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300309770|ref|YP_003773862.1| phosphomethylpyrimidine kinase ...   133   1e-32

>gi|300309770|ref|YP_003773862.1| phosphomethylpyrimidine kinase
           [Herbaspirillum seropedicae SmR1]
          Length = 288

 Score =  133 bits (335), Expect = 1e-32,   Method: Compositional matrix adjust.
 Identities = 65/76 (85%), Positives = 69/76 (90%)

Query: 69  GGAGMQADIPAISALGCHPLSVPTALTVQDNVSVFAVHPIDAELIRHQAQVLIDRFDIRA 128
           GGAGMQADIPAI+ALGCHPLSVPTALTVQDNVSVFAVH +D EL+RHQAQVLIDRFDI A
Sbjct: 22  GGAGMQADIPAITALGCHPLSVPTALTVQDNVSVFAVHALDPELVRHQAQVLIDRFDIAA 81

Query: 129 VKLGIAGNRRNGEXAA 144
           VKLGIAG+R N E  A
Sbjct: 82  VKLGIAGSRENAEVIA 97



 Score =  123 bits (308), Expect = 1e-29,   Method: Compositional matrix adjust.
 Identities = 59/67 (88%), Positives = 63/67 (94%)

Query: 1  MQADIPAISALGCHPLSVPTALTVQDNVSVFAVHPIDAELIRHQAQVLIDRFDIRAVKLG 60
          MQADIPAI+ALGCHPLSVPTALTVQDNVSVFAVH +D EL+RHQAQVLIDRFDI AVKLG
Sbjct: 26 MQADIPAITALGCHPLSVPTALTVQDNVSVFAVHALDPELVRHQAQVLIDRFDIAAVKLG 85

Query: 61 IAGNRRN 67
          IAG+R N
Sbjct: 86 IAGSREN 92


  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    0.135    0.399 

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: 598,372
Number of extensions: 18764
Number of successful extensions: 61
Number of sequences better than 1.0e-08: 1
Number of HSP's gapped: 61
Number of HSP's successfully gapped: 2
Length of query: 237
Length of database: 1,619,870
Length adjustment: 82
Effective length of query: 155
Effective length of database: 1,231,600
Effective search space: 190898000
Effective search space used: 190898000
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: 129 (54.3 bits)