RPS-BLAST 2.2.26 [Sep-21-2011]

Database: scop70_1_75 
           13,730 sequences; 2,407,596 total letters

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

Query= psy16600
         (152 letters)



>d2exfa1 g.40.1.1 (A:12-53) HIV nucleocapsid {Human immunodeficiency
           virus type 1, different isolates [TaxId: 11676]}
          Length = 42

 Score = 47.2 bits (112), Expect = 5e-09
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 77  SIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECP 115
           ++ C+NC   GH ARNC     K C+ C + GH  K+C 
Sbjct: 1   NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39



 Score = 42.2 bits (99), Expect = 4e-07
 Identities = 13/40 (32%), Positives = 21/40 (52%)

Query: 56 SVTCYNCSGQGHVAKDCTVKSSIICYNCNSSGHFARNCPN 95
          +V C+NC  +GH A++C       C+ C   GH  ++C  
Sbjct: 1  NVKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCTE 40



 Score = 37.1 bits (86), Expect = 3e-05
 Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 1/38 (2%)

Query: 37 IVCYKCNNYGHFAREC-ATESVTCYNCSGQGHVAKDCT 73
          + C+ C   GH AR C A     C+ C  +GH  KDCT
Sbjct: 2  VKCFNCGKEGHTARNCRAPRKKGCWKCGKEGHQMKDCT 39



 Score = 31.0 bits (70), Expect = 0.005
 Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 11/47 (23%)

Query: 100 RCYACHQAGHMAKECPGQTAGKSPEPVVDMSLTCYVCGHQGHLSYDC 146
           +C+ C + GH A+ C                  C+ CG +GH   DC
Sbjct: 3   KCFNCGKEGHTARNCRAP-----------RKKGCWKCGKEGHQMKDC 38



 Score = 31.0 bits (70), Expect = 0.006
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 9/46 (19%)

Query: 7  IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 52
          ++C+NC   GH   +C                C+KC   GH  ++C
Sbjct: 2  VKCFNCGKEGHTARNCRAPRK---------KGCWKCGKEGHQMKDC 38



 Score = 23.3 bits (50), Expect = 3.6
 Identities = 6/18 (33%), Positives = 13/18 (72%)

Query: 130 SLTCYVCGHQGHLSYDCK 147
           ++ C+ CG +GH + +C+
Sbjct: 1   NVKCFNCGKEGHTARNCR 18


>d1nc8a_ g.40.1.1 (A:) HIV nucleocapsid {Human immunodeficiency
          virus type 2 [TaxId: 11709]}
          Length = 29

 Score = 26.3 bits (58), Expect = 0.25
 Identities = 9/19 (47%), Positives = 11/19 (57%)

Query: 75 KSSIICYNCNSSGHFARNC 93
          +  I C+NC   GH AR C
Sbjct: 4  RKVIRCWNCGKEGHSARQC 22



 Score = 25.5 bits (56), Expect = 0.51
 Identities = 7/18 (38%), Positives = 12/18 (66%)

Query: 55 ESVTCYNCSGQGHVAKDC 72
          + + C+NC  +GH A+ C
Sbjct: 5  KVIRCWNCGKEGHSARQC 22


>d2f4ma1 d.3.1.4 (A:164-450) Peptide:N-glycanase 1, PNG1 {Mouse (Mus
           musculus) [TaxId: 10090]}
          Length = 287

 Score = 26.5 bits (58), Expect = 1.4
 Identities = 5/50 (10%), Positives = 13/50 (26%)

Query: 1   MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAR 50
               + I C  C      +      +  + +     +  + C+      R
Sbjct: 76  FRWVNNIVCSKCGGETRSRDEALLPNDDELKWGAKNVENHYCDACQLSNR 125


>d1a6bb_ g.40.1.1 (B:) Zinc finger protein ncp10 {Moloney murine
           leukemia virus, MoMLV [TaxId: 11801]}
          Length = 40

 Score = 24.2 bits (52), Expect = 1.5
 Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 1/37 (2%)

Query: 90  ARNCPNDSSKRCYACHQAGHMAKECPGQTAG-KSPEP 125
            R        +C  C + GH AK+CP +  G + P P
Sbjct: 2   ERRRSQLDRDQCAYCKEKGHWAKDCPKKPRGPRGPRP 38



 Score = 22.3 bits (47), Expect = 8.1
 Identities = 7/16 (43%), Positives = 10/16 (62%)

Query: 80 CYNCNSSGHFARNCPN 95
          C  C   GH+A++CP 
Sbjct: 13 CAYCKEKGHWAKDCPK 28


>d1nuia2 g.41.3.2 (A:10-63) Zinc-binding domain of primase-helicase
           {Bacteriophage T7 [TaxId: 10760]}
          Length = 54

 Score = 23.7 bits (51), Expect = 3.3
 Identities = 10/44 (22%), Positives = 18/44 (40%), Gaps = 2/44 (4%)

Query: 80  CYNCNSSGHFARNCPNDSSKRCYACHQAGHMAKECPGQTAGKSP 123
           C NC SS   +    +D    CY C +     ++   + + + P
Sbjct: 8   CDNCGSSDGNSLF--SDGHTFCYVCEKWTAGNEDTKERASKRKP 49


>d2j8ga1 b.109.1.1 (A:191-339) C-terminal domain of endolysin
           {Bacteriophage cp-1 [TaxId: 10747]}
          Length = 149

 Score = 24.8 bits (53), Expect = 3.7
 Identities = 16/105 (15%), Positives = 24/105 (22%), Gaps = 8/105 (7%)

Query: 8   QCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFARECATESVTCYNCSGQGH 67
             +  FD   Y  +                  Y  +N               Y     G 
Sbjct: 38  GVWYYFDSKGYCLTSEWLK-------DNEKWYYLKDNGAMA-TGWVLVGSEWYYMDDSGA 89

Query: 68  VAKDCTVKSSIICYNCNSSGHFARNCPNDSSKRCYACHQAGHMAK 112
           +        +   Y  N  G+   N    S K  Y  +  G +A 
Sbjct: 90  MVTGWVKYKNNWYYMTNERGNMVSNEFIKSGKGWYFMNTNGELAD 134


>d1dsqa_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse
           mammary tumor virus [TaxId: 11757]}
          Length = 26

 Score = 21.9 bits (46), Expect = 7.6
 Identities = 8/15 (53%), Positives = 10/15 (66%)

Query: 133 CYVCGHQGHLSYDCK 147
           C+ CG  GH+  DCK
Sbjct: 5   CFSCGKTGHIKRDCK 19


  Database: scop70_1_75
    Posted date:  Mar 27, 2010  6:21 PM
  Number of letters in database: 2,407,596
  Number of sequences in database:  13,730
  
Lambda     K      H
   0.321    0.132    0.448 

Gapped
Lambda     K      H
   0.267   0.0575    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 575,278
Number of extensions: 26619
Number of successful extensions: 247
Number of sequences better than 10.0: 1
Number of HSP's gapped: 214
Number of HSP's successfully gapped: 102
Length of query: 152
Length of database: 2,407,596
Length adjustment: 78
Effective length of query: 74
Effective length of database: 1,336,656
Effective search space: 98912544
Effective search space used: 98912544
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.0 bits)