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= 041106
         (83 letters)

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

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



>pdb|2O1P|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
           State
 pdb|2O1P|B Chain B, Structure Of Yeast Poly(A) Polymerase In A Somewhat Closed
           State
          Length = 546

 Score = 28.1 bits (61), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 6/37 (16%)

Query: 19  VLTTKNKEASTCADVPKGFLS-VYVG-----ENQKKR 49
           ++T +NKE  +  D PK +LS +Y+G     EN+K++
Sbjct: 442 LVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEK 478


>pdb|1FA0|A Chain A, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
           And 3'-Datp
 pdb|1FA0|B Chain B, Structure Of Yeast Poly(A) Polymerase Bound To Manganate
           And 3'-Datp
 pdb|3C66|A Chain A, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
           80-105
 pdb|3C66|B Chain B, Yeast Poly(A) Polymerase In Complex With Fip1 Residues
           80-105
          Length = 537

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 6/37 (16%)

Query: 19  VLTTKNKEASTCADVPKGFLS-VYVG-----ENQKKR 49
           ++T +NKE  +  D PK +LS +Y+G     EN+K++
Sbjct: 442 LVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEK 478


>pdb|2HHP|A Chain A, Structure Of Yeast Poly(A) Polymerase In A Closed
           Conformation
          Length = 530

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 6/37 (16%)

Query: 19  VLTTKNKEASTCADVPKGFLS-VYVG-----ENQKKR 49
           ++T +NKE  +  D PK +LS +Y+G     EN+K++
Sbjct: 442 LVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEK 478


>pdb|2Q66|A Chain A, Structure Of Yeast Poly(A) Polymerase With Atp And
           Oligo(A)
          Length = 525

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 14/37 (37%), Positives = 24/37 (64%), Gaps = 6/37 (16%)

Query: 19  VLTTKNKEASTCADVPKGFLS-VYVG-----ENQKKR 49
           ++T +NKE  +  D PK +LS +Y+G     EN+K++
Sbjct: 438 LVTDENKEEESIKDAPKAYLSTMYIGLDFNIENKKEK 474


>pdb|3HL2|A Chain A, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
 pdb|3HL2|B Chain B, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
 pdb|3HL2|C Chain C, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
 pdb|3HL2|D Chain D, The Crystal Structure Of The Human Sepsecs-Trnasec Complex
          Length = 501

 Score = 26.2 bits (56), Expect = 4.5,   Method: Compositional matrix adjust.
 Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 13/80 (16%)

Query: 6   LGFIPAKQILPHSVLTTKNKEASTCADVPK-----GFLSVYVGENQKKRFLVPEFGFNYP 60
           L  I A   +PH V      ++S C  + +     G +  +V ++  K F+VP       
Sbjct: 238 LAVICANYDIPHIVNNAYGVQSSKCMHLIQQGARVGRIDAFV-QSLDKNFMVP------- 289

Query: 61  MGASTIPSGQDTFIEVISRL 80
           +G + I    D+FI+ IS++
Sbjct: 290 VGGAIIAGFNDSFIQEISKM 309


>pdb|3B8A|X Chain X, Crystal Structure Of Yeast Hexokinase Pi In Complex With
           Glucose
          Length = 485

 Score = 25.8 bits (55), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 21/61 (34%), Positives = 29/61 (47%), Gaps = 3/61 (4%)

Query: 11  AKQILPHSVLTTKNKEA--STCADVPKGFLSVYVGENQKKRFLVPEFGFNYPMGASTIPS 68
           +K  LPH + TTK++E   S  AD  K F+      N K    +  F F+YP   + I  
Sbjct: 110 SKYKLPHDMRTTKHQEELWSFIADSLKDFMVEQELLNTKDTLPLG-FTFSYPASQNKINE 168

Query: 69  G 69
           G
Sbjct: 169 G 169


  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
   0.320    0.138    0.403 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,389,238
Number of Sequences: 62578
Number of extensions: 86493
Number of successful extensions: 108
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 101
Number of HSP's gapped (non-prelim): 13
length of query: 83
length of database: 14,973,337
effective HSP length: 51
effective length of query: 32
effective length of database: 11,781,859
effective search space: 377019488
effective search space used: 377019488
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)