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= 027896
         (217 letters)

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

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



>pdb|1GCC|A Chain A, Solution Nmr Structure Of The Complex Of Gcc-Box Binding
          Domain Of Aterf1 And Gcc-Box Dna, Minimized Average
          Structure
          Length = 63

 Score = 54.3 bits (129), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 28/61 (45%), Positives = 32/61 (52%), Gaps = 1/61 (1%)

Query: 6  KKFRGVRQRHWGSWVSEIRHPLLK-RRVWLGTFETXXXXXXXXXXXXILMSGRNAKTNFP 64
          K +RGVRQR WG + +EIR P     RVWLGTFET              M G  A  NFP
Sbjct: 1  KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 60

Query: 65 V 65
          +
Sbjct: 61 L 61


>pdb|2GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
          Minimized Mean Structure
 pdb|3GCC|A Chain A, Solution Structure Of The Gcc-Box Binding Domain, Nmr,
          46 Structures
          Length = 70

 Score = 54.3 bits (129), Expect = 5e-08,   Method: Composition-based stats.
 Identities = 29/65 (44%), Positives = 34/65 (52%), Gaps = 1/65 (1%)

Query: 6  KKFRGVRQRHWGSWVSEIRHPLLK-RRVWLGTFETXXXXXXXXXXXXILMSGRNAKTNFP 64
          K +RGVRQR WG + +EIR P     RVWLGTFET              M G  A  NFP
Sbjct: 4  KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFP 63

Query: 65 VTQSS 69
          +  +S
Sbjct: 64 LRVNS 68


>pdb|3CV2|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
           Bacillis Anthracis Malate Synthase A: Comparison With
           Isoform G And Implications For Structure Based Drug
           Design
 pdb|3CV2|B Chain B, Atomic Resolution Structures Of Escherichia Coli And
           Bacillis Anthracis Malate Synthase A: Comparison With
           Isoform G And Implications For Structure Based Drug
           Design
          Length = 532

 Score = 28.5 bits (62), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 41/103 (39%), Gaps = 11/103 (10%)

Query: 113 LDTENSHIGVWQKRAGQRSDSNWVMTVHLGNRNSGDHTNVNNNADDVSGNALPLAADSQS 172
           L+  N H G W    G    +  V    LG+R         N  + +     P+ AD Q 
Sbjct: 354 LEANNGHDGTWIAHPGLADTAMAVFNDILGSRK--------NQLEVMREQDAPITAD-QL 404

Query: 173 QGPELMIRTE--MDDEERIALQMIEELLNRNCPSPSYEVQEKA 213
             P    RTE  M    R+A+Q IE  ++ N   P Y + E A
Sbjct: 405 LAPCDGERTEEGMRANIRVAVQYIEAWISGNGXVPIYGLMEDA 447


>pdb|3CUZ|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
           Bacillis Anthracis Malate Synthase A: Comparison With
           Isoform G And Implications For Structure Based Drug
           Design
 pdb|3CV1|A Chain A, Atomic Resolution Structures Of Escherichia Coli And
           Bacillis Anthracis Malate Synthase A: Comparison With
           Isoform G And Implications For Structure Based Drug
           Design
          Length = 532

 Score = 28.1 bits (61), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 30/103 (29%), Positives = 41/103 (39%), Gaps = 11/103 (10%)

Query: 113 LDTENSHIGVWQKRAGQRSDSNWVMTVHLGNRNSGDHTNVNNNADDVSGNALPLAADSQS 172
           L+  N H G W    G    +  V    LG+R         N  + +     P+ AD Q 
Sbjct: 354 LEANNGHDGTWIAHPGLADTAMAVFNDILGSR--------KNQLEVMREQDAPITAD-QL 404

Query: 173 QGPELMIRTE--MDDEERIALQMIEELLNRNCPSPSYEVQEKA 213
             P    RTE  M    R+A+Q IE  ++ N   P Y + E A
Sbjct: 405 LAPCDGERTEEGMRANIRVAVQYIEAWISGNGCVPIYGLMEDA 447


>pdb|2LSL|A Chain A, Solution Structure Of The C-Terminal Domain Of Tetrahymena
           Telomerase Protein P65
          Length = 137

 Score = 27.3 bits (59), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 22/71 (30%), Positives = 36/71 (50%), Gaps = 19/71 (26%)

Query: 140 HLGNRNSGDHTNVNNNADDVSGNALPLAADSQSQGPEL---------MIRTEMDDEERIA 190
           HLG     D+  ++ N++ ++ N +      Q Q P+L         MIR +  DE+R+A
Sbjct: 41  HLGYEFYCDY--IDENSNQINSNLI-----QQDQHPQLNDLLKEGQAMIRFQNSDEQRLA 93

Query: 191 LQMIEELLNRN 201
           +Q   +LLN N
Sbjct: 94  IQ---KLLNHN 101


  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
   0.313    0.128    0.386 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,926,378
Number of Sequences: 62578
Number of extensions: 204571
Number of successful extensions: 269
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 264
Number of HSP's gapped (non-prelim): 6
length of query: 217
length of database: 14,973,337
effective HSP length: 95
effective length of query: 122
effective length of database: 9,028,427
effective search space: 1101468094
effective search space used: 1101468094
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 49 (23.5 bits)