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= 0001.0412.p
         (286 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 ...   456   e-130
gi|300313137|ref|YP_003777229.1| phosphomethylpyrimidine kinase ...   103   2e-23

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

 Score =  456 bits (1174), Expect = e-130,   Method: Compositional matrix adjust.
 Identities = 233/280 (83%), Positives = 253/280 (90%)

Query: 3   MSAAYRATPPCVLVFSGSDPSGGAGMQADIPAITALGCHPLSVPTALTVQDNVSVFAVHA 62
           M AAYR+TPPCVLVFSGSDPSGGAGMQADIPAITALGCHPLSVPTALTVQDNVSVFAVHA
Sbjct: 1   MQAAYRSTPPCVLVFSGSDPSGGAGMQADIPAITALGCHPLSVPTALTVQDNVSVFAVHA 60

Query: 63  LDPELVRHQAQVLIDRFEIAAVKLGIAGSVENAQMIATLIRQLRQRNAQLPVVLDPVLAN 122
           LDPELVRHQAQVLIDRF+IAAVKLGIAGS ENA++IA LIRQLR+RN QLPVVLDPVLAN
Sbjct: 61  LDPELVRHQAQVLIDRFDIAAVKLGIAGSRENAEVIADLIRQLRERNPQLPVVLDPVLAN 120

Query: 123 GKGDQLSRDDAARIIEPLYALATVITPNLNEARRLCGEVDAARQAALLMQRGCAHVLLKG 182
           GKGDQLSRDDA R+IEPLY LATVITPNLNEARRLCG+V+  +QAALLM RGCAHVLLKG
Sbjct: 121 GKGDQLSRDDAVRVIEPLYELATVITPNLNEARRLCGDVEPTQQAALLMARGCAHVLLKG 180

Query: 183 GHGAQEEDVVNRWYGPAPAAAVPHPISASHSWRWTRLPDEFHGSGCTLAAALSACLARGL 242
           GHG QE+DV+NRWYG    +        +  WRWTRLPDEFHGSGCTLAAALSACLARGL
Sbjct: 181 GHGPQEQDVINRWYGQLFRSEFAEEAIETARWRWTRLPDEFHGSGCTLAAALSACLARGL 240

Query: 243 PMQQALDLAQRYTQHALSSAYAIAPGQRIPNRVPAFEPVV 282
           PM+QA++LAQ YTQHAL+++YAIA GQRIP+RVPAFE VV
Sbjct: 241 PMRQAIELAQHYTQHALATSYAIADGQRIPHRVPAFEAVV 280


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

 Score =  103 bits (257), Expect = 2e-23,   Method: Compositional matrix adjust.
 Identities = 89/279 (31%), Positives = 140/279 (50%), Gaps = 35/279 (12%)

Query: 10  TPPCVLVFSGSDPSGGAGMQADIPAITALGCHPLSVPTALTVQDNVSVFAVHALDPELVR 69
           TPP +L F  +DP G  G+QAD+    A+GCH LSV T+L + D   V  V  ++ + V 
Sbjct: 5   TPPLILSFGAADPVGATGVQADLATYAAMGCHGLSVITSLLIGDTARVEDVQVVEVDWVA 64

Query: 70  HQAQVLIDRFEIAAVKLGIAGSVENAQMIATLIRQLRQRNAQLPVVLDPVLANGKGDQLS 129
            QA+V+++   +AA K+G  GS+EN  +IA ++         +P++LDP   +   +Q  
Sbjct: 65  DQARVILEDMAVAAFKVGNVGSIENISVIAEIVSDY----PDVPLILDP-FTSALANQED 119

Query: 130 RDDAARII---EPLYALATVITPNLNEARRLCGE-----------VDAARQAALLMQRGC 175
            DD  R+I   E L   AT++  +  E  RL              +DA R    +++ GC
Sbjct: 120 EDD--RLIAIRELLIPQATLMVASAGELARLAETWREPVPGDALMLDAMR----IIEMGC 173

Query: 176 AHVLLKGGHGAQEEDVVNRWYGPAPAAAVPHPISASHSWRWTRLPDEFHGSGCTLAAALS 235
            ++L+       +E + N  +  +                W RLP  F G+G TL+AA++
Sbjct: 174 EYLLVTNTQTDLQE-IANSLFDES---------GLVRQDAWQRLPGSFVGAGTTLSAAMA 223

Query: 236 ACLARGLPMQQALDLAQRYTQHALSSAYAIAPGQRIPNR 274
           A LA GL +  A   AQ +T  AL++A  I  G+ +P+R
Sbjct: 224 AMLANGLEVPLAAAEAQEFTLAALANAQRIGMGKLVPDR 262


  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
   0.321    0.134    0.403 

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: 948,347
Number of extensions: 39466
Number of successful extensions: 162
Number of sequences better than 1.0e-08: 2
Number of HSP's gapped: 159
Number of HSP's successfully gapped: 2
Length of query: 286
Length of database: 1,619,870
Length adjustment: 84
Effective length of query: 202
Effective length of database: 1,222,130
Effective search space: 246870260
Effective search space used: 246870260
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: 130 (54.7 bits)