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= 025398
         (253 letters)

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

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



>pdb|2VRD|A Chain A, The Structure Of The Zinc Finger From The Human
          Spliceosomal Protein U1c
          Length = 61

 Score = 34.7 bits (78), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 1/31 (3%)

Query: 12 WCDFCKIYISNNPSSIR-NHDLGQRHKENVQ 41
          +CD+C  Y++++  S+R  H  G++HKENV+
Sbjct: 5  YCDYCDTYLTHDSPSVRKTHCSGRKHKENVK 35


>pdb|3CW1|L Chain L, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|9 Chain 9, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|0 Chain 0, Crystal Structure Of Human Spliceosomal U1 Snrnp
 pdb|3CW1|LL Chain l, Crystal Structure Of Human Spliceosomal U1 Snrnp
          Length = 77

 Score = 34.7 bits (78), Expect = 0.051,   Method: Compositional matrix adjust.
 Identities = 13/31 (41%), Positives = 23/31 (74%), Gaps = 1/31 (3%)

Query: 12 WCDFCKIYISNNPSSIR-NHDLGQRHKENVQ 41
          +CD+C  Y++++  S+R  H  G++HKENV+
Sbjct: 5  YCDYCDTYLTHDSPSVRKTHCSGRKHKENVK 35


>pdb|2NOV|A Chain A, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
           Structure Of A Gram-Positive Quinolone Target
 pdb|2NOV|B Chain B, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
           Structure Of A Gram-Positive Quinolone Target
 pdb|2NOV|C Chain C, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
           Structure Of A Gram-Positive Quinolone Target
 pdb|2NOV|D Chain D, Breakage-Reunion Domain Of S.Pneumoniae Topo Iv: Crystal
           Structure Of A Gram-Positive Quinolone Target
 pdb|3FOE|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
           Of Type Iia Topoisomerases
 pdb|3FOE|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
           Of Type Iia Topoisomerases
 pdb|3FOF|A Chain A, Structural Insight Into The Quinolone-Dna Cleavage Complex
           Of Type Iia Topoisomerases
 pdb|3FOF|B Chain B, Structural Insight Into The Quinolone-Dna Cleavage Complex
           Of Type Iia Topoisomerases
 pdb|3K9F|A Chain A, Detailed Structural Insight Into The Quinolone-Dna
           Cleavage Complex Of Type Iia Topoisomerases
 pdb|3K9F|B Chain B, Detailed Structural Insight Into The Quinolone-Dna
           Cleavage Complex Of Type Iia Topoisomerases
 pdb|3KSA|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
           Of Type Iia Topoisomerases (Cleaved Form)
 pdb|3KSA|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
           Of Type Iia Topoisomerases (Cleaved Form)
 pdb|3KSB|A Chain A, Detailed Structural Insight Into The Dna Cleavage Complex
           Of Type Iia Topoisomerases (Re-Sealed Form)
 pdb|3KSB|B Chain B, Detailed Structural Insight Into The Dna Cleavage Complex
           Of Type Iia Topoisomerases (Re-Sealed Form)
 pdb|3LTN|A Chain A, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
           (S. Pneumoniae)
 pdb|3LTN|B Chain B, Inhibitor-Stabilized Topoisomerase Iv-Dna Cleavage Complex
           (S. Pneumoniae)
 pdb|3RAF|A Chain A, Quinazolinedione-Dna Cleavage Complex Of Type Iv
           Topoisomerase From S. Pneumoniae
 pdb|3RAF|B Chain B, Quinazolinedione-Dna Cleavage Complex Of Type Iv
           Topoisomerase From S. Pneumoniae
 pdb|3RAD|A Chain A, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
           Topoisomerase From S. Pneumoniae
 pdb|3RAD|B Chain B, Quinolone(Clinafloxacin)-Dna Cleavage Complex Of Type Iv
           Topoisomerase From S. Pneumoniae
 pdb|3RAE|A Chain A, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
           Topoisomerase From S. Pneumoniae
 pdb|3RAE|B Chain B, Quinolone(Levofloxacin)-Dna Cleavage Complex Of Type Iv
           Topoisomerase From S. Pneumoniae
          Length = 496

 Score = 30.0 bits (66), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 16/57 (28%), Positives = 26/57 (45%)

Query: 157 PFPAFGGGSIVENKDSAKSQNGPARGPVVSSSLNPMRSVKGAPSSLAVGKRKREDNK 213
           P P F  G+I++ +D  K      +G VV  S   +  +KG    + + +   E NK
Sbjct: 209 PGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINK 265


  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
   0.311    0.128    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,134,196
Number of Sequences: 62578
Number of extensions: 281073
Number of successful extensions: 516
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 511
Number of HSP's gapped (non-prelim): 4
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 50 (23.9 bits)