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= 036165
         (566 letters)

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

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



>pdb|2PHG|A Chain A, Model For Vp16 Binding To Tfiib
          Length = 206

 Score = 32.3 bits (72), Expect = 0.72,   Method: Compositional matrix adjust.
 Identities = 27/116 (23%), Positives = 49/116 (42%), Gaps = 16/116 (13%)

Query: 433 DEAIELFNQMEERKKLDHLSFTAVLTACCHVGLVELGQRLFNMMQEKYKIMPRTEHYACM 492
           D    LF Q+ E+K L   +  A+ +AC ++   + G             +PRT    C 
Sbjct: 26  DRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEG-------------VPRTFKEICA 72

Query: 493 VDLLGRAGRLAEAYEMI-KTMSTEPDLFVWGALLGA-CKNHGNIELAEIAAKHLSE 546
           V  + +   +   +++I K + T  DL   G  +   C N    +  ++AA H++ 
Sbjct: 73  VSRISK-KEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIAR 127


>pdb|1TFB|A Chain A, Nmr Studies Of Human General Transcription Factor Tfiib:
           Dynamics And Interaction With Vp16 Activation Domain, 20
           Structures
          Length = 208

 Score = 32.3 bits (72), Expect = 0.77,   Method: Compositional matrix adjust.
 Identities = 27/116 (23%), Positives = 49/116 (42%), Gaps = 16/116 (13%)

Query: 433 DEAIELFNQMEERKKLDHLSFTAVLTACCHVGLVELGQRLFNMMQEKYKIMPRTEHYACM 492
           D    LF Q+ E+K L   +  A+ +AC ++   + G             +PRT    C 
Sbjct: 28  DRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEG-------------VPRTFKEICA 74

Query: 493 VDLLGRAGRLAEAYEMI-KTMSTEPDLFVWGALLGA-CKNHGNIELAEIAAKHLSE 546
           V  + +   +   +++I K + T  DL   G  +   C N    +  ++AA H++ 
Sbjct: 75  VSRISK-KEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIAR 129


>pdb|1C9B|A Chain A, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
           Core Domain Complex Bound To An Extended, Modified
           Adenoviral Major Late Promoter (Admlp)
 pdb|1C9B|E Chain E, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
           Core Domain Complex Bound To An Extended, Modified
           Adenoviral Major Late Promoter (Admlp)
 pdb|1C9B|I Chain I, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
           Core Domain Complex Bound To An Extended, Modified
           Adenoviral Major Late Promoter (Admlp)
 pdb|1C9B|M Chain M, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
           Core Domain Complex Bound To An Extended, Modified
           Adenoviral Major Late Promoter (Admlp)
 pdb|1C9B|Q Chain Q, Crystal Structure Of A Human Tbp Core Domain-Human Tfiib
           Core Domain Complex Bound To An Extended, Modified
           Adenoviral Major Late Promoter (Admlp)
          Length = 207

 Score = 32.3 bits (72), Expect = 0.79,   Method: Compositional matrix adjust.
 Identities = 27/116 (23%), Positives = 49/116 (42%), Gaps = 16/116 (13%)

Query: 433 DEAIELFNQMEERKKLDHLSFTAVLTACCHVGLVELGQRLFNMMQEKYKIMPRTEHYACM 492
           D    LF Q+ E+K L   +  A+ +AC ++   + G             +PRT    C 
Sbjct: 27  DRTNNLFKQVYEQKSLKGRANDAIASACLYIACRQEG-------------VPRTFKEICA 73

Query: 493 VDLLGRAGRLAEAYEMI-KTMSTEPDLFVWGALLGA-CKNHGNIELAEIAAKHLSE 546
           V  + +   +   +++I K + T  DL   G  +   C N    +  ++AA H++ 
Sbjct: 74  VSRISK-KEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIAR 128


>pdb|1VOL|A Chain A, Tfiib (Human Core Domain)TBP (A.THALIANA)TATA ELEMENT
           Ternary Complex
          Length = 204

 Score = 31.6 bits (70), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 27/116 (23%), Positives = 48/116 (41%), Gaps = 16/116 (13%)

Query: 433 DEAIELFNQMEERKKLDHLSFTAVLTACCHVGLVELGQRLFNMMQEKYKIMPRTEHYACM 492
           D    LF Q  E+K L   +  A+ +AC ++   + G             +PRT    C 
Sbjct: 24  DRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEG-------------VPRTFKEICA 70

Query: 493 VDLLGRAGRLAEAYEMI-KTMSTEPDLFVWGALLGA-CKNHGNIELAEIAAKHLSE 546
           V  + +   +   +++I K + T  DL   G  +   C N    +  ++AA H++ 
Sbjct: 71  VSRISK-KEIGRCFKLILKALETSVDLITTGDFMSRFCSNLCLPKQVQMAATHIAR 125


>pdb|4B1M|A Chain A, Carbohydrate Binding Module Cbm66 From Bacillus Subtilis
 pdb|4B1M|B Chain B, Carbohydrate Binding Module Cbm66 From Bacillus Subtilis
 pdb|4B1M|C Chain C, Carbohydrate Binding Module Cbm66 From Bacillus Subtilis
          Length = 185

 Score = 31.2 bits (69), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 63  AHYKMPI-ISRSFHLSPAAYSERIEIYIRDR 92
           A YK PI +++ +HL   A  +R +IY+ DR
Sbjct: 122 AEYKTPIDVNKKYHLKTEAEGDRFKIYLDDR 152


>pdb|4B1L|A Chain A, Carbohydrate Binding Module Cbm66 From Bacillus Subtilis
          Length = 165

 Score = 31.2 bits (69), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 63  AHYKMPI-ISRSFHLSPAAYSERIEIYIRDR 92
           A YK PI +++ +HL   A  +R +IY+ DR
Sbjct: 102 AEYKTPIDVNKKYHLKTEAEGDRFKIYLDDR 132


>pdb|4AZZ|A Chain A, Carbohydrate Binding Module Cbm66 From Bacillus Subtilis
 pdb|4AZZ|B Chain B, Carbohydrate Binding Module Cbm66 From Bacillus Subtilis
          Length = 172

 Score = 31.2 bits (69), Expect = 1.8,   Method: Composition-based stats.
 Identities = 13/31 (41%), Positives = 20/31 (64%), Gaps = 1/31 (3%)

Query: 63  AHYKMPI-ISRSFHLSPAAYSERIEIYIRDR 92
           A YK PI +++ +HL   A  +R +IY+ DR
Sbjct: 101 AEYKTPIDVNKKYHLKTEAEGDRFKIYLDDR 131


>pdb|1AYZ|A Chain A, Crystal Structure Of The Saccharomyces Cerevisiae
           Ubiquitin- Conjugating Enzyme Rad6 (Ubc2) At 2.6a
           Resolution
 pdb|1AYZ|B Chain B, Crystal Structure Of The Saccharomyces Cerevisiae
           Ubiquitin- Conjugating Enzyme Rad6 (Ubc2) At 2.6a
           Resolution
 pdb|1AYZ|C Chain C, Crystal Structure Of The Saccharomyces Cerevisiae
           Ubiquitin- Conjugating Enzyme Rad6 (Ubc2) At 2.6a
           Resolution
          Length = 169

 Score = 29.6 bits (65), Expect = 4.9,   Method: Composition-based stats.
 Identities = 18/68 (26%), Positives = 32/68 (47%), Gaps = 5/68 (7%)

Query: 415 NTVTWNSMIFGCANHGYCDEAIELFNQMEER--KKLDHLSFTAVLTACCHVGLVELGQRL 472
           N + WN+MI G A+  Y D    L  + +E    K  H+ F   L+   H  +   G+  
Sbjct: 32  NVMVWNAMIIGPADTPYEDGTFRLLLEFDEEYPNKPPHVKF---LSEMFHPNVYANGEIC 88

Query: 473 FNMMQEKY 480
            +++Q ++
Sbjct: 89  LDILQNRW 96


  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
   0.323    0.135    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,740,490
Number of Sequences: 62578
Number of extensions: 614696
Number of successful extensions: 1286
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 1283
Number of HSP's gapped (non-prelim): 9
length of query: 566
length of database: 14,973,337
effective HSP length: 104
effective length of query: 462
effective length of database: 8,465,225
effective search space: 3910933950
effective search space used: 3910933950
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)