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= 026877
         (231 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 (274), Expect = 8e-25,   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 = 9e-19,   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


>pdb|1T9K|A Chain A, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
           Translation Initiation Factor [thermotoga Maritima]
 pdb|1T9K|B Chain B, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
           Translation Initiation Factor [thermotoga Maritima]
 pdb|1T9K|C Chain C, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
           Translation Initiation Factor [thermotoga Maritima]
 pdb|1T9K|D Chain D, X-ray Crystal Structure Of Aif-2b Alpha Subunit-related
           Translation Initiation Factor [thermotoga Maritima]
          Length = 347

 Score = 27.3 bits (59), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 34/76 (44%), Gaps = 12/76 (15%)

Query: 114 RDVALLLDKGFKAQERCFFHPLSNDMSISLNTNDLDKFLKSIGRDPAYVDLEANPAVGKD 173
           R  A+ L       E+ FF         + +  +L + L++     AY D+E N A+GK+
Sbjct: 90  RPTAVNLFWALNRXEKVFFE--------NADRENLFEILENEALKXAYEDIEVNKAIGKN 141

Query: 174 QPPDLAAFVPSGSTVL 189
                A  +  GST+L
Sbjct: 142 G----AQLIKDGSTIL 153


  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
   0.316    0.134    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,771,109
Number of Sequences: 62578
Number of extensions: 276564
Number of successful extensions: 657
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 650
Number of HSP's gapped (non-prelim): 11
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)