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= 023979
         (274 letters)

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

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



>pdb|3NVQ|A Chain A, Molecular Mechanism Of Guidance Cue Recognition
 pdb|3NVQ|E Chain E, Molecular Mechanism Of Guidance Cue Recognition
          Length = 590

 Score = 34.7 bits (78), Expect = 0.055,   Method: Compositional matrix adjust.
 Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 3/71 (4%)

Query: 80  EVELYYKFDMRDKAAFQRIVMNQTLYLVQRFTWNKATQSWELYSNVPRDLCDTYALCGAY 139
           E E  + F++ +   F+R    QT+ L         +  WE+ S VP DLC+ Y   G +
Sbjct: 400 EQEHSFAFNIMEIQPFRRAAAIQTMSLDAERRKLYVSSQWEV-SQVPLDLCEVYG-GGCH 457

Query: 140 GICIISDMPVC 150
           G C++S  P C
Sbjct: 458 G-CLMSRDPYC 467


>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 = 27.3 bits (59), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 26/50 (52%), Gaps = 3/50 (6%)

Query: 172 RDKSLNYSRQDGFIKFTAMKLPDATLSWVSKSMNLNECREKCLDNSSCMA 221
           RD+++N  ++      T  +L    L W+ KS  ++E +E C D  S MA
Sbjct: 110 RDENVNVVKKAIL---TMTQLYKVALQWMVKSRVISELQEACWDMVSAMA 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
   0.322    0.137    0.453 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,074,735
Number of Sequences: 62578
Number of extensions: 385802
Number of successful extensions: 743
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 742
Number of HSP's gapped (non-prelim): 8
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)