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= 0001.3745.p
         (279 letters)

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

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

gi|300313137|ref|YP_003777229.1| phosphomethylpyrimidine kinase ...   470   e-134
gi|300309770|ref|YP_003773862.1| phosphomethylpyrimidine kinase ...   115   4e-27

>gi|300313137|ref|YP_003777229.1| phosphomethylpyrimidine kinase
           [Herbaspirillum seropedicae SmR1]
          Length = 282

 Score =  470 bits (1209), Expect = e-134,   Method: Compositional matrix adjust.
 Identities = 255/282 (90%), Positives = 269/282 (95%), Gaps = 3/282 (1%)

Query: 1   VQNQTPPLILTFGAADPVGATGVQADLATFAAMGCHGLSVVTALLIGDTARVEDVQVVEV 60
           +QNQTPPLIL+FGAADPVGATGVQADLAT+AAMGCHGLSV+T+LLIGDTARVEDVQVVEV
Sbjct: 1   MQNQTPPLILSFGAADPVGATGVQADLATYAAMGCHGLSVITSLLIGDTARVEDVQVVEV 60

Query: 61  DWVADQARVILEDMAVSAFKVGALGSIENISVIAEIVSDYPDVPLILDPFISALANQEDE 120
           DWVADQARVILEDMAV+AFKVG +GSIENISVIAEIVSDYPDVPLILDPF SALANQEDE
Sbjct: 61  DWVADQARVILEDMAVAAFKVGNVGSIENISVIAEIVSDYPDVPLILDPFTSALANQEDE 120

Query: 121 DDRLIAIRELLIPQATVLVCSAGELTRLAETWREPALGDTLMLDAMRIIELGCEYLLVTN 180
           DDRLIAIRELLIPQAT++V SAGEL RLAETWREP  GD LMLDAMRIIE+GCEYLLVTN
Sbjct: 121 DDRLIAIRELLIPQATLMVASAGELARLAETWREPVPGDALMLDAMRIIEMGCEYLLVTN 180

Query: 181 TQTDLQEVANSLFDESGLVRQDAWPRLPGSFVGAGTTLSAAMAAMLANDLEAPLAASEAQ 240
           TQTDLQE+ANSLFDESGLVRQDAW RLPGSFVGAGTTLSAAMAAMLAN LE PLAA+EAQ
Sbjct: 181 TQTDLQEIANSLFDESGLVRQDAWQRLPGSFVGAGTTLSAAMAAMLANGLEVPLAAAEAQ 240

Query: 241 EFTLAALANAQRIGMGKLLPDRYFWARESEDP---NAPPSLN 279
           EFTLAALANAQRIGMGKL+PDRYFWARESEDP   +APPSLN
Sbjct: 241 EFTLAALANAQRIGMGKLVPDRYFWARESEDPTDLDAPPSLN 282


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

 Score =  115 bits (288), Expect = 4e-27,   Method: Compositional matrix adjust.
 Identities = 90/274 (32%), Positives = 136/274 (49%), Gaps = 25/274 (9%)

Query: 5   TPPLILTFGAADPVGATGVQADLATFAAMGCHGLSVVTALLIGDTARVEDVQVVEVDWVA 64
           TPP +L F  +DP G  G+QAD+    A+GCH LSV TAL + D   V  V  ++ + V 
Sbjct: 8   TPPCVLVFSGSDPSGGAGMQADIPAITALGCHPLSVPTALTVQDNVSVFAVHALDPELVR 67

Query: 65  DQARVILEDMAVSAFKVGALGSIENISVIAEIVSDY----PDVPLILDPFISALANQEDE 120
            QA+V+++   ++A K+G  GS EN  VIA+++       P +P++LDP ++     +  
Sbjct: 68  HQAQVLIDRFDIAAVKLGIAGSRENAEVIADLIRQLRERNPQLPVVLDPVLANGKGDQLS 127

Query: 121 DDRLIAIRELLIPQATVLVCSAGELTRLAETWREPALGDTLMLDAMRIIELGCEYLLVTN 180
            D  + + E L   ATV+  +  E  RL     EP     L++        GC ++L+  
Sbjct: 128 RDDAVRVIEPLYELATVITPNLNEARRLCGDV-EPTQQAALLM------ARGCAHVLLKG 180

Query: 181 TQ-TDLQEVANSLFDESGLVRQD-----------AWPRLPGSFVGAGTTLSAAMAAMLAN 228
                 Q+V N  + +  L R +            W RLP  F G+G TL+AA++A LA 
Sbjct: 181 GHGPQEQDVINRWYGQ--LFRSEFAEEAIETARWRWTRLPDEFHGSGCTLAAALSACLAR 238

Query: 229 DLEAPLAASEAQEFTLAALANAQRIGMGKLLPDR 262
            L    A   AQ +T  ALA +  I  G+ +P R
Sbjct: 239 GLPMRQAIELAQHYTQHALATSYAIADGQRIPHR 272


  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
   0.318    0.133    0.383 

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: 763,440
Number of extensions: 26858
Number of successful extensions: 109
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 107
Number of HSP's successfully gapped: 2
Length of query: 279
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 195
Effective length of database: 1,222,130
Effective search space: 238315350
Effective search space used: 238315350
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 (21.7 bits)
S2: 130 (54.7 bits)