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= 004600
         (743 letters)

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

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



>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
           Type4 (Pad4)
          Length = 670

 Score = 29.3 bits (64), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 535 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 571


>pdb|4DKT|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With
           N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1e)-2-
           Fluoroethanimidoyl]-L-Ornithinamide
          Length = 668

 Score = 29.3 bits (64), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 533 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 569


>pdb|1WD9|A Chain A, Calcium Bound Form Of Human Peptidylarginine Deiminase
           Type4 (pad4)
 pdb|1WDA|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase
           Type4 (Pad4) In Complex With Benzoyl-L-Arginine Amide
          Length = 670

 Score = 29.3 bits (64), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 535 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 571


>pdb|2DW5|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With
           N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine
           Amide
 pdb|3B1T|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With O-Cl-Amidine
 pdb|3B1U|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With O-F-Amidine
          Length = 671

 Score = 29.3 bits (64), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 536 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 572


>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
          Length = 666

 Score = 29.3 bits (64), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 531 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 567


>pdb|2DEW|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With Histone H3 N-Terminal Tail Including Arg8
 pdb|2DEX|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With Histone H3 N-Terminal Peptide Including
           Arg17
 pdb|2DEY|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
           Complex With Histone H4 N-Terminal Tail Including Arg3
          Length = 671

 Score = 29.3 bits (64), Expect = 9.2,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 536 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 572


>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
          Length = 666

 Score = 28.9 bits (63), Expect = 9.5,   Method: Compositional matrix adjust.
 Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 2/37 (5%)

Query: 335 NFADNRALIDHSARVMRVITWNRSF--RGLGLPHAEI 369
           N   N+ L +H++ V R I WNR    R LGL  ++I
Sbjct: 531 NILSNKTLREHNSFVERCIDWNRELLKRELGLAESDI 567


  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
   0.315    0.128    0.362 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,537,538
Number of Sequences: 62578
Number of extensions: 595787
Number of successful extensions: 1430
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 1430
Number of HSP's gapped (non-prelim): 7
length of query: 743
length of database: 14,973,337
effective HSP length: 106
effective length of query: 637
effective length of database: 8,340,069
effective search space: 5312623953
effective search space used: 5312623953
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: 55 (25.8 bits)