RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16623
         (93 letters)



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

 Score = 37.9 bits (88), Expect = 4e-06
 Identities = 12/46 (26%), Positives = 19/46 (41%), Gaps = 9/46 (19%)

Query: 42 IQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAREC 87
          ++C+NC   GH   +C                C+KC   GH  ++C
Sbjct: 2  VKCFNCGKEGHTARNCRAPRK---------KGCWKCGKEGHQMKDC 38



 Score = 22.5 bits (48), Expect = 3.7
 Identities = 5/17 (29%), Positives = 8/17 (47%)

Query: 44 CYNCFDFGHYQYSCPQK 60
          C+ C   GH    C ++
Sbjct: 25 CWKCGKEGHQMKDCTER 41


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

 Score = 25.8 bits (56), Expect = 0.17
 Identities = 9/20 (45%), Positives = 11/20 (55%)

Query: 71 GIVCYKCNNYGHFARECATE 90
          G VC+ C   GH  R+C  E
Sbjct: 2  GPVCFSCGKTGHIKRDCKEE 21


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

 Score = 26.2 bits (57), Expect = 0.68
 Identities = 5/50 (10%), Positives = 13/50 (26%)

Query: 36  MSSTSTIQCYNCFDFGHYQYSCPQKSSADARGDKVGIVCYKCNNYGHFAR 85
               + 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 = 0.78
 Identities = 8/18 (44%), Positives = 11/18 (61%)

Query: 43 QCYNCFDFGHYQYSCPQK 60
          QC  C + GH+   CP+K
Sbjct: 12 QCAYCKEKGHWAKDCPKK 29



 Score = 21.9 bits (46), Expect = 6.4
 Identities = 6/14 (42%), Positives = 9/14 (64%)

Query: 74 CYKCNNYGHFAREC 87
          C  C   GH+A++C
Sbjct: 13 CAYCKEKGHWAKDC 26


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

 Score = 23.2 bits (50), Expect = 1.4
 Identities = 8/16 (50%), Positives = 10/16 (62%)

Query: 72 IVCYKCNNYGHFAREC 87
          I C+ C   GH AR+C
Sbjct: 7  IRCWNCGKEGHSARQC 22



 Score = 21.7 bits (46), Expect = 6.0
 Identities = 7/17 (41%), Positives = 9/17 (52%)

Query: 41 TIQCYNCFDFGHYQYSC 57
           I+C+NC   GH    C
Sbjct: 6  VIRCWNCGKEGHSARQC 22


>d1aoca_ g.17.1.5 (A:) Coagulogen {Japanese horseshoe crab
          (Tachypleus tridentatus) [TaxId: 6853]}
          Length = 175

 Score = 25.0 bits (54), Expect = 1.6
 Identities = 7/21 (33%), Positives = 11/21 (52%)

Query: 43 QCYNCFDFGHYQYSCPQKSSA 63
          +CYN   F H++  CP  +  
Sbjct: 74 RCYNFPPFTHFKSECPVSTRD 94


>d1gph11 c.61.1.1 (1:235-465) Glutamine PRPP amidotransferase,
           C-terminal domain {Bacillus subtilis [TaxId: 1423]}
          Length = 231

 Score = 23.8 bits (51), Expect = 3.6
 Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 10  WNNYVLGILLIIKQRNEGLLFVLRVEMSSTSTIQCYNCFDFGHY 53
                +G   +     EGLL  +  +   ++  QC  CF  G Y
Sbjct: 169 EIRQEIGADTLSFLSVEGLLKGIGRKYDDSNCGQCLACFT-GKY 211


>d1dsva_ g.40.1.1 (A:) Nucleic acid binding protein p14 {Mouse
          mammary tumor virus [TaxId: 11757]}
          Length = 31

 Score = 21.3 bits (45), Expect = 8.4
 Identities = 5/15 (33%), Positives = 8/15 (53%)

Query: 73 VCYKCNNYGHFAREC 87
          +C +C    H+  EC
Sbjct: 4  LCPRCKKGYHWKSEC 18


>d1cl4a_ g.40.1.1 (A:) Nucleocapsid protein from mason-pfizer
          monkey virus (MPMV) {Mason-pfizer monkey virus [TaxId:
          11855]}
          Length = 32

 Score = 21.3 bits (45), Expect = 9.2
 Identities = 6/15 (40%), Positives = 9/15 (60%)

Query: 73 VCYKCNNYGHFAREC 87
          +C +C    H+A EC
Sbjct: 4  LCPRCKRGKHWANEC 18


  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
   0.323    0.136    0.438 

Gapped
Lambda     K      H
   0.267   0.0617    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 333,466
Number of extensions: 12480
Number of successful extensions: 64
Number of sequences better than 10.0: 1
Number of HSP's gapped: 63
Number of HSP's successfully gapped: 24
Length of query: 93
Length of database: 2,407,596
Length adjustment: 56
Effective length of query: 37
Effective length of database: 1,638,716
Effective search space: 60632492
Effective search space used: 60632492
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 47 (22.1 bits)