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= 023523
         (281 letters)

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

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



>pdb|1NVP|B Chain B, Human TfiiaTBPDNA COMPLEX
          Length = 57

 Score = 45.8 bits (107), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/50 (44%), Positives = 34/50 (68%)

Query: 3  TSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGVI 52
          T+    +Y  VIEDVI+ VRD F+++G  E VL EL+ +WE K++Q+  +
Sbjct: 6  TNTVPKLYRSVIEDVINDVRDIFLDDGVDEQVLMELKTLWENKLMQSRAV 55


>pdb|1RM1|C Chain C, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex
          Length = 286

 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 31/51 (60%)

Query: 1  MATSATGMVYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          M+ +    VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V
Sbjct: 1  MSNAEASRVYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKV 51


>pdb|1YTF|B Chain B, Yeast TfiiaTBPDNA COMPLEX
 pdb|1NH2|B Chain B, Crystal Structure Of A Yeast TfiiaTBPDNA COMPLEX
          Length = 53

 Score = 38.5 bits (88), Expect = 0.004,   Method: Composition-based stats.
 Identities = 16/43 (37%), Positives = 28/43 (65%)

Query: 9  VYIRVIEDVISKVRDEFVNNGPGESVLNELQGIWEMKMIQAGV 51
          VY  ++E V+++VR++F N G  E  L +L+ IW+ K+ +  V
Sbjct: 8  VYEIIVESVVNEVREDFENAGIDEQTLQDLKNIWQKKLTETKV 50


>pdb|1V10|A Chain A, Structure Of Rigidoporus Lignosus Laccase From
           Hemihedrally Twinned Crystals
          Length = 521

 Score = 29.3 bits (64), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 16/35 (45%), Positives = 18/35 (51%)

Query: 198 GTSHQPLTQDFFTMSAGKRKREDFPAQYHNGGYNI 232
           G SHQPLT D  T+ AG+R      A    G Y I
Sbjct: 251 GVSHQPLTVDSLTIFAGQRYSVVVEANQAVGNYWI 285


>pdb|1A5F|L Chain L, Fab Fragment Of A Monoclonal Anti-E-Selectin Antibody
          Length = 220

 Score = 28.5 bits (62), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 10/73 (13%)

Query: 209 FTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSS 268
           FT+S    + ED    Y    YN P   GAG  +    EL+    +P     +  F  SS
Sbjct: 77  FTLSISGVQAEDLAVYYCQNNYNYPLTFGAGTKL----ELKRADAAP----TVSIFPPSS 128

Query: 269 HQMDAG--AVDCF 279
            Q+ +G  +V CF
Sbjct: 129 EQLTSGGASVVCF 141


>pdb|1BBD|L Chain L, Three Dimensional Structure Of The Fab Fragment Of A
           Neutralizing Antibody To Human Rhinovirus Serotype 2
 pdb|1A3R|L Chain L, Fab Fragment (Antibody 8f5) Complexed With Peptide From
           Human Rhinovirus (Serotype 2) Viral Capsid Protein Vp2
           (Residues 156-170)
          Length = 220

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 10/73 (13%)

Query: 209 FTMSAGKRKREDFPAQYHNGGYNIPQQDGAGDAMSEIFELEVRFLSPLLIYALLYFSKSS 268
           FT+S    + ED    Y    YN P   GAG  +    EL+    +P     +  F  SS
Sbjct: 77  FTLSISGVQAEDLAVYYCQNNYNYPLTFGAGTKL----ELKRADAAP----TVSIFPPSS 128

Query: 269 HQMDAG--AVDCF 279
            Q+ +G  +V CF
Sbjct: 129 EQLTSGGASVVCF 141


>pdb|3HMU|A Chain A, Crystal Structure Of A Class Iii Aminotransferase From
          Silicibacter Pomeroyi
 pdb|3HMU|B Chain B, Crystal Structure Of A Class Iii Aminotransferase From
          Silicibacter Pomeroyi
          Length = 472

 Score = 28.5 bits (62), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 9/26 (34%), Positives = 18/26 (69%)

Query: 17 VISKVRDEFVNNGPGESVLNELQGIW 42
          VI++ R  ++N+  GE +L+ + G+W
Sbjct: 40 VITRARGVWLNDSEGEEILDAMAGLW 65


  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    0.132    0.385 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,878,639
Number of Sequences: 62578
Number of extensions: 243474
Number of successful extensions: 309
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 301
Number of HSP's gapped (non-prelim): 10
length of query: 281
length of database: 14,973,337
effective HSP length: 98
effective length of query: 183
effective length of database: 8,840,693
effective search space: 1617846819
effective search space used: 1617846819
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: 51 (24.3 bits)