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= 007424
         (604 letters)

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

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



>pdb|3O2T|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human
           Symplekin
          Length = 386

 Score = 29.6 bits (65), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 9   VNGLLNK--LSDRDTYSQAAKELDSIAATVDPTLLPTFLSCILSTNSSDKPGVRKECIHV 66
           V  LLN+  L   D+     K++  +    DPTLL  FL  I++  +     VRK  I  
Sbjct: 27  VVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGF 86

Query: 67  IATLSNSHNLSPYITKIINSITRNFRDKNSALQATCISTVSSL 109
           I            + K+I ++    RD+N  +    I T++ L
Sbjct: 87  IEEACKRD--IELLLKLIANLNMLLRDENVNVVKKAILTMTQL 127


>pdb|3ODR|A Chain A, Crystal Structure Of The N-Terminal Domain Of Human
           Symplekin
          Length = 415

 Score = 29.3 bits (64), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 9   VNGLLNK--LSDRDTYSQAAKELDSIAATVDPTLLPTFLSCILSTNSSDKPGVRKECIHV 66
           V  LLN+  L   D+     K++  +    DPTLL  FL  I++  +     VRK  I  
Sbjct: 56  VVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGF 115

Query: 67  IATLSNSHNLSPYITKIINSITRNFRDKNSALQATCISTVSSL 109
           I            + K+I ++    RD+N  +    I T++ L
Sbjct: 116 IEEACKRD--IELLLKLIANLNMLLRDENVNVVKKAILTMTQL 156


>pdb|3O2Q|A Chain A, Crystal Structure Of The Human Symplekin-Ssu72-Ctd
           Phosphopeptide Complex
 pdb|3O2Q|D Chain D, Crystal Structure Of The Human Symplekin-Ssu72-Ctd
           Phosphopeptide Complex
 pdb|3O2S|A Chain A, Crystal Structure Of The Human Symplekin-Ssu72 Complex
 pdb|4H3H|A Chain A, Crystal Structure Of A Ternary Complex Of Human Symplekin
           Ntd, Human Ssu72 And A Rna Poymerase Ii Ctd Peptide
           Phosphorylated At Ser-7
 pdb|4H3H|D Chain D, Crystal Structure Of A Ternary Complex Of Human Symplekin
           Ntd, Human Ssu72 And A Rna Poymerase Ii Ctd Peptide
           Phosphorylated At Ser-7
 pdb|4H3K|A Chain A, Crystal Structure Of A Ternary Complex Of Human Symplekin
           Ntd, Human Ssu72 And A Rna Polymerase Ii Ctd Peptide
           Phosphorylated At Ser-2, Ser-5 And Ser-7
 pdb|4H3K|D Chain D, Crystal Structure Of A Ternary Complex Of Human Symplekin
           Ntd, Human Ssu72 And A Rna Polymerase Ii Ctd Peptide
           Phosphorylated At Ser-2, Ser-5 And Ser-7
          Length = 351

 Score = 29.3 bits (64), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 9   VNGLLNK--LSDRDTYSQAAKELDSIAATVDPTLLPTFLSCILSTNSSDKPGVRKECIHV 66
           V  LLN+  L   D+     K++  +    DPTLL  FL  I++  +     VRK  I  
Sbjct: 27  VVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGF 86

Query: 67  IATLSNSHNLSPYITKIINSITRNFRDKNSALQATCISTVSSL 109
           I            + K+I ++    RD+N  +    I T++ L
Sbjct: 87  IEEACKRD--IELLLKLIANLNMLLRDENVNVVKKAILTMTQL 127


>pdb|3ODS|A Chain A, Crystal Structure Of The K185a Mutant Of The N-Terminal
           Domain Of Human Symplekin
          Length = 415

 Score = 29.3 bits (64), Expect = 6.2,   Method: Compositional matrix adjust.
 Identities = 28/103 (27%), Positives = 44/103 (42%), Gaps = 4/103 (3%)

Query: 9   VNGLLNK--LSDRDTYSQAAKELDSIAATVDPTLLPTFLSCILSTNSSDKPGVRKECIHV 66
           V  LLN+  L   D+     K++  +    DPTLL  FL  I++  +     VRK  I  
Sbjct: 56  VVDLLNQAALITNDSKITVLKQVQELIINKDPTLLDNFLDEIIAFQADKSIEVRKFVIGF 115

Query: 67  IATLSNSHNLSPYITKIINSITRNFRDKNSALQATCISTVSSL 109
           I            + K+I ++    RD+N  +    I T++ L
Sbjct: 116 IEEACKRD--IELLLKLIANLNMLLRDENVNVVKKAILTMTQL 156


  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    0.129    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,551,396
Number of Sequences: 62578
Number of extensions: 517169
Number of successful extensions: 1106
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1106
Number of HSP's gapped (non-prelim): 5
length of query: 604
length of database: 14,973,337
effective HSP length: 104
effective length of query: 500
effective length of database: 8,465,225
effective search space: 4232612500
effective search space used: 4232612500
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: 54 (25.4 bits)