BLASTP 2.2.26 [Sep-21-2011]


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= 020246
         (329 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|1VJF|A Chain A, Crystal Structure Of A Putative Dna-Binding Protein
           (Cc_0111) From Caulobacter Crescentus Cb15 At 1.62 A
           Resolution
          Length = 180

 Score =  110 bits (275), Expect = 1e-24,   Method: Compositional matrix adjust.
 Identities = 60/168 (35%), Positives = 91/168 (54%), Gaps = 2/168 (1%)

Query: 4   SKDQLLARLKDLQIEFSQYEHPAVMTVEAQAKYVGNIGGGLSKNLFLKDKKHRFYIVSAL 63
           ++  L A      ++    +HP V  VE   +      GG +KNLFLKD K + +++SAL
Sbjct: 15  TRADLFAFFDAHGVDHKTLDHPPVFRVEEGLEIKAAXPGGHTKNLFLKDAKGQLWLISAL 74

Query: 64  ADTKVDMKVLSQRLGLGKGGLRMAPEETMLEILKVPLGSVTPFALVNESARDVALLLDKG 123
            +T +D+K L   +G G+  L   P+E  LE L V  GSVT F L+N++ + V  +LDK 
Sbjct: 75  GETTIDLKKLHHVIGSGR--LSFGPQEXXLETLGVTPGSVTAFGLINDTEKRVRFVLDKA 132

Query: 124 FKAQERCFFHPLSNDMSISLNTNDLDKFLKSIGRDPAYVDLEANPAVG 171
               +   FHPL ND + +++   L +FL ++G +P  VD  A   VG
Sbjct: 133 LADSDPVNFHPLKNDATTAVSQAGLRRFLAALGVEPXIVDFAAXEVVG 180


>pdb|1VKI|A Chain A, Crystal Structure Of A Putative Oligo-Nucleotide Binding
           Protein (Atu3699, Agr_l_2275) From Agrobacterium
           Tumefaciens Str. C58 At 1.60 A Resolution
 pdb|1VKI|B Chain B, Crystal Structure Of A Putative Oligo-Nucleotide Binding
           Protein (Atu3699, Agr_l_2275) From Agrobacterium
           Tumefaciens Str. C58 At 1.60 A Resolution
          Length = 181

 Score = 90.1 bits (222), Expect = 1e-18,   Method: Compositional matrix adjust.
 Identities = 53/153 (34%), Positives = 81/153 (52%), Gaps = 1/153 (0%)

Query: 7   QLLARLKDLQIEFSQYEHPAVMTVEAQAKYVGNIGGGLSKNLFLKDKKHRFYIVSALADT 66
           +L   L  L I  +  +H  V TV         I GG +KNLF+KDKK ++++++   + 
Sbjct: 23  ELFEFLDGLGISHTTKQHEPVFTVAESQSLRDLIPGGHTKNLFVKDKKDQYFVLTVEENA 82

Query: 67  KVDMKVLSQRLGLGKGGLRMAPEETMLEILKVPLGSVTPFALVNESARDVALLLDKGFKA 126
            VD+K + + +G     +     E MLE L V  GSVT F  +N++AR V  +LD     
Sbjct: 83  VVDLKSVHKTIG-AASRVSFGRPEKMLEYLGVVPGSVTVFGAINDTARQVTFVLDSDLLE 141

Query: 127 QERCFFHPLSNDMSISLNTNDLDKFLKSIGRDP 159
            E    HPLSND + ++ + DL +FL++ G  P
Sbjct: 142 NELVNGHPLSNDQTTTIASKDLIRFLEATGHAP 174


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.315    0.131    0.368 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,315,882
Number of Sequences: 62578
Number of extensions: 375515
Number of successful extensions: 788
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 784
Number of HSP's gapped (non-prelim): 7
length of query: 329
length of database: 14,973,337
effective HSP length: 99
effective length of query: 230
effective length of database: 8,778,115
effective search space: 2018966450
effective search space used: 2018966450
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 52 (24.6 bits)