RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780125|ref|YP_003064538.1| prophage antirepressor
[Candidatus Liberibacter asiaticus str. psy62]
         (262 letters)



>d2tnfa_ b.22.1.1 (A:) Tumor necrosis factor (TNF) {Mouse (Mus
           musculus) [TaxId: 10090]}
          Length = 148

 Score = 27.7 bits (61), Expect = 1.2
 Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 3/30 (10%)

Query: 228 DVPMQHVEG---STQQLKWNSNLLVSFLQN 254
           D P+ HV       +QL+W S    + L N
Sbjct: 2   DKPVAHVVANHQVEEQLEWLSQRANALLAN 31


>d1s21a_ d.166.1.4 (A:) AvrPphF ORF2, a type III effector
           {Pseudomonas syringae pv. phaseolicola [TaxId: 319]}
          Length = 176

 Score = 27.2 bits (60), Expect = 1.3
 Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 178 TITQIGERLNPPQRARFLNKLLLKRGLQVSKVSGGYRPTPKGEERGGKMCDVP 230
           T+T I  +L+  +R  FL+     R   ++  +  YR T +   R G     P
Sbjct: 9   TLTSI-HQLSSEERENFLDAHDPMRVYDLNSETSVYRTTQREYVRNGYATGNP 60


>d1tnra_ b.22.1.1 (A:) Tumor necrosis factor (TNF) {Human (Homo
           sapiens) [TaxId: 9606]}
          Length = 144

 Score = 26.5 bits (58), Expect = 2.1
 Identities = 9/30 (30%), Positives = 13/30 (43%), Gaps = 3/30 (10%)

Query: 230 PMQHVEG---STQQLKWNSNLLVSFLQNEL 256
           P  H+ G       L W +N   +FLQ+  
Sbjct: 2   PAAHLIGDPSKQNSLLWRANTDRAFLQDGF 31


>d2dk8a1 a.4.5.85 (A:8-75) DNA-directed RNA polymerase III subunit
           RPC6, RPO3F {Mouse (Mus musculus) [TaxId: 10090]}
          Length = 68

 Score = 26.3 bits (58), Expect = 2.6
 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 2/31 (6%)

Query: 186 LNPPQRARFLNKLLLKRGLQVSKVSGG--YR 214
           +   QRA  +N+LL    L + + + G  YR
Sbjct: 35  IEAQQRAVAINRLLSMGQLDLLRSNTGLLYR 65


>d1y0ua_ a.4.5.5 (A:) Putative arsenical resistance operon repressor
           AF0168 {Archaeoglobus fulgidus [TaxId: 2234]}
          Length = 89

 Score = 25.0 bits (54), Expect = 7.6
 Identities = 5/22 (22%), Positives = 11/22 (50%)

Query: 199 LLKRGLQVSKVSGGYRPTPKGE 220
           +L+ G  + +V   +  T  G+
Sbjct: 66  VLEAGFCIERVGERWVVTDAGK 87


>d1xm5a_ d.92.1.15 (A:) Hypothetical protein YbeY {Escherichia coli
           [TaxId: 562]}
          Length = 152

 Score = 24.6 bits (53), Expect = 7.9
 Identities = 6/27 (22%), Positives = 14/27 (51%), Gaps = 1/27 (3%)

Query: 83  LPSAQKFERWVFEEVLPTLRKTGSYSV 109
           LP   +F+ W+   V+P  ++    ++
Sbjct: 18  LPEESQFQTWL-NAVIPQFQEESEVTI 43


>d1vjya_ d.144.1.7 (A:) Type I TGF-beta receptor R4 {Human (Homo
           sapiens) [TaxId: 9606]}
          Length = 303

 Score = 24.8 bits (53), Expect = 8.5
 Identities = 15/51 (29%), Positives = 22/51 (43%), Gaps = 5/51 (9%)

Query: 90  ERWVFEEVLPTLRKTGSYSVEA-PKLRATSASTVLRVHKHLEELAKQAGLK 139
            RW   E L  + K       A    R T+     R+ K L +L++Q G+K
Sbjct: 256 NRWQSCEALRVMAKIMRECWYANGAARLTAL----RIKKTLSQLSQQEGIK 302


>d3bofa1 c.1.21.2 (A:301-560) Cobalamin-dependent methionine
           synthase MetH, C-terminal domain {Thermotoga maritima
           [TaxId: 2336]}
          Length = 260

 Score = 24.6 bits (53), Expect = 9.2
 Identities = 7/18 (38%), Positives = 11/18 (61%)

Query: 182 IGERLNPPQRARFLNKLL 199
           IGER+NP  R +   ++ 
Sbjct: 18  IGERINPAGRKKLWAEMQ 35


  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
   0.315    0.132    0.378 

Gapped
Lambda     K      H
   0.267   0.0539    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 920,302
Number of extensions: 41243
Number of successful extensions: 116
Number of sequences better than 10.0: 1
Number of HSP's gapped: 116
Number of HSP's successfully gapped: 12
Length of query: 262
Length of database: 2,407,596
Length adjustment: 84
Effective length of query: 178
Effective length of database: 1,254,276
Effective search space: 223261128
Effective search space used: 223261128
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.2 bits)