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= 000404
         (1562 letters)

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

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



>pdb|1MM2|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b
 pdb|2L75|A Chain A, Solution Structure Of Chd4-Phd2 In Complex With H3k9me3
          Length = 61

 Score = 31.6 bits (70), Expect = 3.2,   Method: Composition-based stats.
 Identities = 11/28 (39%), Positives = 20/28 (71%), Gaps = 2/28 (7%)

Query: 830 PSTFHQNCLD--IKKFPSGKWHCVYCSC 855
           PS++H +CL+  + + P+G+W C  C+C
Sbjct: 28  PSSYHIHCLNPPLPEIPNGEWLCPRCTC 55


>pdb|1MM3|A Chain A, Solution Structure Of The 2nd Phd Domain From Mi2b With C-
           Terminal Loop Replaced By Corresponding Loop From Wstf
          Length = 61

 Score = 31.2 bits (69), Expect = 5.4,   Method: Composition-based stats.
 Identities = 11/28 (39%), Positives = 18/28 (64%), Gaps = 2/28 (7%)

Query: 830 PSTFHQNCLD--IKKFPSGKWHCVYCSC 855
           PS++H +CL   + + P G+W C  C+C
Sbjct: 28  PSSYHIHCLRPALYEVPDGEWQCPRCTC 55


>pdb|2L5U|A Chain A, Structure Of The First Phd Finger (Phd1) From Chd4 (Mi2b)
          Length = 61

 Score = 30.4 bits (67), Expect = 7.7,   Method: Composition-based stats.
 Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 2/26 (7%)

Query: 830 PSTFHQNCLD--IKKFPSGKWHCVYC 853
           P  +H  CLD  ++K P GKW C +C
Sbjct: 30  PRAYHMVCLDPDMEKAPEGKWSCPHC 55


>pdb|3FFZ|A Chain A, Domain Organization In Clostridium Butulinum Neurotoxin
           Type E Is Unique: Its Implication In Faster
           Translocation
 pdb|3FFZ|B Chain B, Domain Organization In Clostridium Butulinum Neurotoxin
           Type E Is Unique: Its Implication In Faster
           Translocation
          Length = 1252

 Score = 30.4 bits (67), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 24/75 (32%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 20  SERENEVNDEKKNLFDLNDETTEKEDSGSTSPKETMEIKEIDEKASDECGETGLGENDRN 79
           SE    ++DEK NL   ND    K DS  TS  E  ++ E++     +  +   GEN+ N
Sbjct: 477 SESAPGLSDEKLNLTIQNDAYIPKYDSNGTSDIEQHDVNELNVFFYLDAQKVPEGENNVN 536

Query: 80  -SSRVDCVVKEDSKV 93
            +S +D  + E  K+
Sbjct: 537 LTSSIDTALLEQPKI 551


  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
   0.313    0.131    0.381 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 44,700,826
Number of Sequences: 62578
Number of extensions: 1865696
Number of successful extensions: 2860
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2854
Number of HSP's gapped (non-prelim): 16
length of query: 1562
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1450
effective length of database: 7,964,601
effective search space: 11548671450
effective search space used: 11548671450
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.9 bits)