RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 027581
         (221 letters)



>d2gycc1 c.22.1.1 (C:1-198) Ribosomal protein L4 {Escherichia coli
           [TaxId: 562]}
          Length = 198

 Score = 95.5 bits (237), Expect = 3e-25
 Identities = 35/107 (32%), Positives = 56/107 (52%), Gaps = 2/107 (1%)

Query: 108 NEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGT 167
            + +  + ++   F     + ++H+VV    A  +QGT + KT +EV+G+GKKPWRQKGT
Sbjct: 6   KDAQSALTVSETTFGRDFNEALVHQVVVAYAAGARQGTRAQKTRAEVTGSGKKPWRQKGT 65

Query: 168 GRARHGTLRGPQGWYYNARSKAQKPC-YKVEQEGAAAWVEDCSICSS 213
           GRAR G+++ P  W     + A +P  +  +           SI S 
Sbjct: 66  GRARSGSIKSPI-WRSGGVTFAARPQDHSQKVNKKMYRGALKSILSE 111


>d2zjrc1 c.22.1.1 (C:2-198) Ribosomal protein L4 {Deinococcus
           radiodurans [TaxId: 1299]}
          Length = 197

 Score = 92.1 bits (228), Expect = 8e-24
 Identities = 32/101 (31%), Positives = 51/101 (50%), Gaps = 1/101 (0%)

Query: 117 AGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKKPWRQKGTGRARHGTLR 176
             ++    +   ++H VV WQLA R++GT ST+T ++VS TG+K + QKGTG ARHG   
Sbjct: 13  TIELPLPEVNSGVLHEVVTWQLASRRRGTASTRTRAQVSKTGRKMYGQKGTGNARHGDRS 72

Query: 177 GPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSICSSSRRK 217
            P  +     +   KP                ++  +SR++
Sbjct: 73  VPT-FVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQE 112


>d1dmga_ c.22.1.1 (A:) Ribosomal protein L4 {Thermotoga maritima
           [TaxId: 2336]}
          Length = 225

 Score = 90.2 bits (223), Expect = 7e-23
 Identities = 39/92 (42%), Positives = 54/92 (58%), Gaps = 1/92 (1%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           + + N   E  G + ++  VF++    D++ R V  QL+ R+ GT STKT  EVSG G+K
Sbjct: 3   VDLLNVKGEKVGTLEISDFVFNIDPNYDVMWRYVDMQLSNRRAGTASTKTRGEVSGGGRK 62

Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKP 192
           PW QK TGRARHG++R P  W +       KP
Sbjct: 63  PWPQKHTGRARHGSIRSPI-WRHGGVVHGPKP 93


>d1vqoc1 c.22.1.1 (C:1-246) Ribosomal protein L4 {Archaeon
           Haloarcula marismortui [TaxId: 2238]}
          Length = 246

 Score = 85.6 bits (211), Expect = 5e-21
 Identities = 20/97 (20%), Positives = 34/97 (35%), Gaps = 4/97 (4%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKT--ISEVSGTG 158
             + +      G + L  DVF+ P+R D+I + VR   A R+Q   S +   +   + + 
Sbjct: 3   ATIYDLDGNTDGEVDLP-DVFETPVRSDLIGKAVRAAQANRKQDYGSDEYAGLRTPAESF 61

Query: 159 KKPWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYK 195
                Q    +      R PQ       +   K    
Sbjct: 62  GSGRGQAHVPKLDGRARRVPQ-AVKGRSAHPPKTEKD 97


>d2j01f1 c.22.1.1 (F:1-208) Ribosomal protein L4 {Thermus
           thermophilus [TaxId: 274]}
          Length = 208

 Score = 83.7 bits (206), Expect = 1e-20
 Identities = 39/95 (41%), Positives = 49/95 (51%), Gaps = 6/95 (6%)

Query: 101 IPVTNFFNEDKGFMVLAGDVFDVPIRKDIIHRVVRWQLAKRQQGTHSTKTISEVSGTGKK 160
           IPV +      G   LA       I   ++  VVRWQLAKR++GT STKT  EV+ +G+K
Sbjct: 9   IPVLSP----SGRRELA-ADLPAEINPHLLWEVVRWQLAKRRRGTASTKTRGEVAYSGRK 63

Query: 161 PWRQKGTGRARHGTLRGPQGWYYNARSKAQKPCYK 195
            W QK TGRARHG +  P  +         KP   
Sbjct: 64  IWPQKHTGRARHGDIGAPI-FVGGGVVFGPKPRDY 97


>d1ji9a_ g.46.1.1 (A:) Metallothionein {Mouse (Mus musculus) [TaxId:
           10090]}
          Length = 37

 Score = 24.3 bits (52), Expect = 2.3
 Identities = 11/24 (45%), Positives = 12/24 (50%)

Query: 188 KAQKPCYKVEQEGAAAWVEDCSIC 211
           K  K C    +EGA A  E CS C
Sbjct: 13  KCAKDCVCKGEEGAKAEAEKCSCC 36


>d1c16a2 d.19.1.1 (A:1-180) Class I MHC homolog {Mouse (Mus
           musculus), t22 [TaxId: 10090]}
          Length = 164

 Score = 25.4 bits (55), Expect = 5.0
 Identities = 8/39 (20%), Positives = 17/39 (43%)

Query: 173 GTLRGPQGWYYNARSKAQKPCYKVEQEGAAAWVEDCSIC 211
           G +   Q   ++++ +  +    +EQE A  W +   I 
Sbjct: 26  GYVDDMQVLRFSSKEETPRMAPWLEQEEADNWEQQTRIV 64


>d1k4ta3 e.15.1.1 (A:201-430) Eukaryotic DNA topoisomerase I,
           N-terminal DNA-binding fragment {Human (Homo sapiens)
           [TaxId: 9606]}
          Length = 230

 Score = 25.1 bits (55), Expect = 6.5
 Identities = 9/29 (31%), Positives = 15/29 (51%)

Query: 74  GAFPSDLLLKKTVLTPDITIGLHQDLVIP 102
           G  P   +LK+ ++  DI I   +D  +P
Sbjct: 165 GNHPKMGMLKRRIMPEDIIINCSKDAKVP 193


>d1oisa_ e.15.1.1 (A:) Eukaryotic DNA topoisomerase I, N-terminal
           DNA-binding fragment {Baker's yeast (Saccharomyces
           cerevisiae) [TaxId: 4932]}
          Length = 223

 Score = 25.1 bits (55), Expect = 7.8
 Identities = 11/29 (37%), Positives = 15/29 (51%)

Query: 74  GAFPSDLLLKKTVLTPDITIGLHQDLVIP 102
           GA P    LK+ V   DI + L +D  +P
Sbjct: 157 GAHPKTGKLKRRVNPEDIVLNLSKDAPVP 185


  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
   0.320    0.135    0.411 

Gapped
Lambda     K      H
   0.267   0.0523    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 826,486
Number of extensions: 36416
Number of successful extensions: 59
Number of sequences better than 10.0: 1
Number of HSP's gapped: 58
Number of HSP's successfully gapped: 9
Length of query: 221
Length of database: 2,407,596
Length adjustment: 82
Effective length of query: 139
Effective length of database: 1,281,736
Effective search space: 178161304
Effective search space used: 178161304
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 (21.8 bits)
S2: 51 (23.9 bits)