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= 021645
         (309 letters)

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

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



>pdb|3PSI|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(239-1451)
          Length = 1219

 Score = 33.9 bits (76), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 26/41 (63%), Gaps = 1/41 (2%)

Query: 234 KMVEVSALNHL-MSTHILHQAQQIEHLYEQAVEATKNVELG 273
           KMVE  +LN L +  H+  QAQ IEHL++ A+E T   ++ 
Sbjct: 411 KMVEAESLNLLSVKLHMSSQAQYIEHLFQIALETTNTSDIA 451


>pdb|3PSF|A Chain A, Crystal Structure Of The Spt6 Core Domain From
           Saccharomyces Cerevisiae, Form Spt6(236-1259)
          Length = 1030

 Score = 33.9 bits (76), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 26/41 (63%), Gaps = 1/41 (2%)

Query: 234 KMVEVSALNHL-MSTHILHQAQQIEHLYEQAVEATKNVELG 273
           KMVE  +LN L +  H+  QAQ IEHL++ A+E T   ++ 
Sbjct: 414 KMVEAESLNLLSVKLHMSSQAQYIEHLFQIALETTNTSDIA 454


>pdb|4DDQ|A Chain A, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|B Chain B, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|C Chain C, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|D Chain D, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|E Chain E, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
 pdb|4DDQ|F Chain F, Structural Plasticity Of The Bacillus Subtilis Gyra
           Homodimer
          Length = 502

 Score = 31.2 bits (69), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 4/52 (7%)

Query: 59  GALEQFILNHRKDY----VEMQRTTEQERDSIEHEVTAFIKTCKEQIDILQN 106
           G +EQF L  ++      + +QR T  ER+ IE E  + +K   E  DIL N
Sbjct: 409 GLIEQFSLTEKQAQAILDMRLQRLTGLEREKIEEEYQSLVKLIAELKDILAN 460


>pdb|4ABN|A Chain A, Crystal Structure Of Full Length Mouse Strap (Ttc5)
 pdb|4ABN|B Chain B, Crystal Structure Of Full Length Mouse Strap (Ttc5)
          Length = 474

 Score = 29.3 bits (64), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 6/55 (10%)

Query: 195 LDEIQPEPLTVQQQLLDDETRALQVELTSLLDAVQQTETKMVEVSALNHLMSTHI 249
           LD   PEP   +QQLL+  +R     LTSLL++  +T+ K ++ S L  L   H+
Sbjct: 287 LDPAWPEPQQREQQLLEFLSR-----LTSLLESKGKTKPKKLQ-SMLGSLRPAHL 335


>pdb|1SI2|A Chain A, Crystal Structure Of The Paz Domain Of Human Eif2c1 In
           Complex With A 9-Mer Sirna-Like Duplex Of
           Deoxynucleotide Overhang
          Length = 149

 Score = 28.9 bits (63), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 23/33 (69%), Gaps = 2/33 (6%)

Query: 191 DIRELDEIQPEPLTVQQQL-LDDETRALQVELT 222
           DIR +DE QP+PLT  Q++    E + L+VE+T
Sbjct: 17  DIRNIDE-QPKPLTDSQRVRFTKEIKGLKVEVT 48


>pdb|1SI3|A Chain A, Crystal Structure Of The Paz Domain Of Human Eif2c1 In
           Complex With A 9-Mer Sirna-Like Duplex
          Length = 149

 Score = 28.9 bits (63), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 16/33 (48%), Positives = 23/33 (69%), Gaps = 2/33 (6%)

Query: 191 DIRELDEIQPEPLTVQQQL-LDDETRALQVELT 222
           DIR +DE QP+PLT  Q++    E + L+VE+T
Sbjct: 17  DIRNIDE-QPKPLTDSQRVRFTKEIKGLKVEVT 48


  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    0.127    0.344 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,965,414
Number of Sequences: 62578
Number of extensions: 235227
Number of successful extensions: 784
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 783
Number of HSP's gapped (non-prelim): 12
length of query: 309
length of database: 14,973,337
effective HSP length: 99
effective length of query: 210
effective length of database: 8,778,115
effective search space: 1843404150
effective search space used: 1843404150
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)