TBLASTN 2.2.17 [Aug-26-2007]


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 composition-based statistics:
Schaffer, Alejandro A., L. Aravind, Thomas L. Madden,
Sergei Shavirin, John L. Spouge, Yuri I. Wolf,  
Eugene V. Koonin, and Stephen F. Altschul (2001), 
"Improving the accuracy of PSI-BLAST protein database searches with 
composition-based statistics and other refinements",  Nucleic Acids Res. 29:2994-3005.

Query= EMBOSS_001_1
         (135 letters)

Database: cds.fa 
           5106 sequences; 11,140,562 total letters

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



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

Plasmodium_knowlesi_strain_H|PK4.chr13|PKH_132320|Annotation|Pla...   167   5e-43
Plasmodium_knowlesi_strain_H|PK4.chr12.pseudo|PKH_124970|Annotat...    24   9.9  

>Plasmodium_knowlesi_strain_H|PK4.chr13|PKH_132320|Annotation|Plasmo
           dium_knowlesi_Sanger|(protein coding) hypothetical
           protein, conserved in Plasmodium species
          Length = 396

 Score =  167 bits (424), Expect = 5e-43,   Method: Composition-based stats.
 Identities = 109/132 (82%), Positives = 109/132 (82%)
 Frame = +1

Query: 1   MDREGNNAPTKGVDLLSVKNVILLVLGVTSFILIYKFMKYRKKVSEFERKNKIDEKMKMS 60
           MDREGNNAPTKGVDLLSVKNVILLVLGVTSFILIYKFMKYRKKVSEFERKNKIDEKMKMS
Sbjct: 1   MDREGNNAPTKGVDLLSVKNVILLVLGVTSFILIYKFMKYRKKVSEFERKNKIDEKMKMS 180

Query: 61  REKRLQELEKEMIVNKEKMREQMNKGXXXXXXXXXXXXXXXXXXXXXXFSHFRDLSNYYR 120
           REKRLQELEKEMIVNKEKMREQMNKG                      FSHFRDLSNYYR
Sbjct: 181 REKRLQELEKEMIVNKEKMREQMNKGNDKKDKALDSDKAKPDSKDNSSFSHFRDLSNYYR 360

Query: 121 PSIRNRLCEKLX 132
           PSIRNRLCEKL 
Sbjct: 361 PSIRNRLCEKL* 396


>Plasmodium_knowlesi_strain_H|PK4.chr12.pseudo|PKH_124970|Annotation
           |Plasmodium_knowlesi_Sanger|(protein coding)
           hypothetical protein, conserved in Plasmodium species
          Length = 2646

 Score = 24.3 bits (51), Expect = 9.9,   Method: Composition-based stats.
 Identities = 17/49 (34%), Positives = 30/49 (61%), Gaps = 3/49 (6%)
 Frame = +1

Query: 39  KYRKKVSEFERK-NKIDEKMKMSREKRL--QELEKEMIVNKEKMREQMN 84
           ++ KK+ E ++     DE +K+ R+  +  +EL+KEMI N   +REQ +
Sbjct: 451 EWNKKIEELKKYIGSKDEFIKLERKLTVTSEELKKEMIDNMSSLREQQD 597


  Database: cds.fa
    Posted date:  Mar 10, 2008  2:42 PM
  Number of letters in database: 11,140,562
  Number of sequences in database:  5106
  
Lambda     K      H
   0.325    0.139    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 5106
Number of Hits to DB: 1,171,097
Number of extensions: 11153
Number of successful extensions: 264
Number of sequences better than 10.0: 46
Number of HSP's gapped: 255
Number of HSP's successfully gapped: 54
Length of query: 135
Length of database: 3,713,520
Length adjustment: 82
Effective length of query: 53
Effective length of database: 3,294,828
Effective search space: 174625884
Effective search space used: 174625884
Neighboring words threshold: 13
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 36 (18.5 bits)