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= 001312
         (1102 letters)

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

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



>pdb|2BL6|A Chain A, Solution Structure Of The Zn Complex Of Eiav Ncp11(22-58)
           Peptide, Including Two Cchc Zn-Binding Motifs
          Length = 37

 Score = 38.9 bits (89), Expect = 0.016,   Method: Composition-based stats.
 Identities = 14/23 (60%), Positives = 17/23 (73%)

Query: 951 SPVDAPKVCYKCKKAGHLSKDCK 973
           S   APKVC+KCK+ GH SK C+
Sbjct: 14  SQCRAPKVCFKCKQPGHFSKQCR 36


>pdb|1DSQ|A Chain A, Structure Of The Mmtv Nucleocapsid Protein (Zinc Finger 1)
          Length = 21

 Score = 32.3 bits (72), Expect = 1.4,   Method: Composition-based stats.
 Identities = 10/17 (58%), Positives = 13/17 (76%)

Query: 958 VCYKCKKAGHLSKDCKE 974
           VC+ C K GH+ +DCKE
Sbjct: 4   VCFSCGKTGHIKRDCKE 20


>pdb|1CL4|A Chain A, Nucleocapsid Protein From Mason-Pfizer Monkey Virus (Mpmv)
          Length = 60

 Score = 32.3 bits (72), Expect = 1.5,   Method: Composition-based stats.
 Identities = 10/22 (45%), Positives = 16/22 (72%)

Query: 959 CYKCKKAGHLSKDCKEHPDDSS 980
           C+KC K GH +K+C EH  +++
Sbjct: 4   CFKCGKKGHFAKNCHEHAHNNA 25


>pdb|2DQ3|A Chain A, Crystal Structure Of Aq_298
 pdb|2DQ3|B Chain B, Crystal Structure Of Aq_298
          Length = 425

 Score = 30.8 bits (68), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 4/66 (6%)

Query: 344 RSREFV----KFETFDAALDEFYSKIESQRAEQQHKAKEDAAFHKLNKIHMDQENRVHTL 399
           R +E V    K    D    E   ++E+ R+E+   +KE     +  K   + +NRV  L
Sbjct: 21  RDKELVSLVDKVLELDKRRREIIKRLEALRSERNKLSKEIGKLKREGKDTTEIQNRVKEL 80

Query: 400 KQEVDR 405
           K+E+DR
Sbjct: 81  KEEIDR 86


  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    0.132    0.380 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 31,212,708
Number of Sequences: 62578
Number of extensions: 1274280
Number of successful extensions: 2830
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 2822
Number of HSP's gapped (non-prelim): 13
length of query: 1102
length of database: 14,973,337
effective HSP length: 109
effective length of query: 993
effective length of database: 8,152,335
effective search space: 8095268655
effective search space used: 8095268655
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: 57 (26.6 bits)