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= 037910
         (235 letters)

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

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



>pdb|2DME|A Chain A, Solution Structure Of The Tfiis Domain Ii Of Human Phd
           Finger Protein 3
          Length = 120

 Score = 46.6 bits (109), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 21/39 (53%), Positives = 28/39 (71%)

Query: 165 FLFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE 203
            +FN+KDPKN   ++KVL GEV P+ L+   PEE+AS E
Sbjct: 69  LMFNLKDPKNNILFKKVLKGEVTPDHLIRMSPEELASKE 107


>pdb|2LW4|A Chain A, Solution Nmr Structure Of Human Transcription Elongation
           Factor A Protein 2, Central Domain, Northeast Structural
           Genomics Consortium (Nesg) Target Hr8682b
          Length = 113

 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 19/38 (50%), Positives = 24/38 (63%)

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE 203
           + N+KD KNPD  R VL G + P+ +     EEMASDE
Sbjct: 67  ISNLKDAKNPDLRRNVLCGAITPQQIAVMTSEEMASDE 104


>pdb|3NDQ|A Chain A, Structure Of Human Tfiis Domain Ii
          Length = 108

 Score = 39.7 bits (91), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 31/98 (31%), Positives = 46/98 (46%), Gaps = 7/98 (7%)

Query: 111 SDATRTLIRERLAEAF----SKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC-PF 165
           SD+ R   RE LA A       +A   +E E   Q+   + +   +    + +KN     
Sbjct: 13  SDSVRLKCREMLAAALRTGDDYIAIGADEEELGSQIE--EAIYQEIRNTDMKYKNRVRSR 70

Query: 166 LFNVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDE 203
           + N+KD KNP+  + VL G + P+       EEMASDE
Sbjct: 71  ISNLKDAKNPNLRKNVLCGNIPPDLFARMTAEEMASDE 108


>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
          Length = 178

 Score = 27.7 bits (60), Expect = 5.1,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMA 200
           NV    NPD   K+  G++ PE L T   +++A
Sbjct: 74  NVISKNNPDLKHKIANGDITPEFLATCDAKDLA 106


>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
          Length = 179

 Score = 27.7 bits (60), Expect = 5.8,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMA 200
           NV    NPD   K+  G++ PE L T   +++A
Sbjct: 75  NVISKNNPDLKHKIANGDITPEFLATCDAKDLA 107


>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
          Length = 173

 Score = 27.7 bits (60), Expect = 6.0,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMA 200
           NV    NPD   K+  G++ PE L T   +++A
Sbjct: 69  NVISKNNPDLKHKIANGDITPEFLATCDAKDLA 101


>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
          Length = 309

 Score = 27.7 bits (60), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMA 200
           NV    NPD   K+  G++ PE L T   +++A
Sbjct: 205 NVISKNNPDLKHKIANGDITPEFLATCDAKDLA 237


>pdb|1ENW|A Chain A, Elongation Factor Tfiis Domain Ii
          Length = 114

 Score = 27.3 bits (59), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 12/33 (36%), Positives = 18/33 (54%)

Query: 168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMA 200
           NV    NPD   K+  G++ PE L T   +++A
Sbjct: 79  NVISKNNPDLKHKIANGDITPEFLATCDAKDLA 111


  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
   0.314    0.130    0.363 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,353,209
Number of Sequences: 62578
Number of extensions: 226236
Number of successful extensions: 444
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 435
Number of HSP's gapped (non-prelim): 15
length of query: 235
length of database: 14,973,337
effective HSP length: 96
effective length of query: 139
effective length of database: 8,965,849
effective search space: 1246253011
effective search space used: 1246253011
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 50 (23.9 bits)