RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 025562
         (251 letters)



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

 Score =  115 bits (288), Expect = 3e-32
 Identities = 43/122 (35%), Positives = 71/122 (58%)

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

Query: 168 GRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKVSLSVSLS 227
           GRAR G+++ P +R G      +P+ H+ K+NKK+ R  LK  LS    + ++ +    S
Sbjct: 66  GRARSGSIKSPIWRSGGVTFAARPQDHSQKVNKKMYRGALKSILSELVRQDRLIVVEKFS 125

Query: 228 LF 229
           + 
Sbjct: 126 VE 127


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

 Score =  114 bits (285), Expect = 1e-31
 Identities = 56/120 (46%), Positives = 79/120 (65%)

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

Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
           PW QK TGRARHG++R P +R G  +HGPKPR  + KLNKK+++L L+ ALS +  E K+
Sbjct: 63  PWPQKHTGRARHGSIRSPIWRHGGVVHGPKPRDWSKKLNKKMKKLALRSALSVKYRENKL 122


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

 Score =  112 bits (282), Expect = 6e-31
 Identities = 33/123 (26%), Positives = 54/123 (43%), Gaps = 4/123 (3%)

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

Query: 159 KKPWRQKGTGRARHGTLRGPQFRGGTTMHGPKP-RSHAIKLNKKVRRLGLKIALSARAAE 217
                Q    +      R PQ   G + H PK  +  ++ LN K R+L ++ AL+A A  
Sbjct: 62  GSGRGQAHVPKLDGRARRVPQAVKGRSAHPPKTEKDRSLDLNDKERQLAVRSALAATADA 121

Query: 218 GKV 220
             V
Sbjct: 122 DLV 124


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

 Score =  109 bits (274), Expect = 3e-30
 Identities = 47/104 (45%), Positives = 68/104 (65%)

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

Query: 177 GPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
            P F GG    GPKPRS+   L ++VR+LGL +A+++R   GK+
Sbjct: 73  VPTFVGGGVAFGPKPRSYDYTLPRQVRQLGLAMAIASRQEGGKL 116


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

 Score = 97.6 bits (242), Expect = 2e-25
 Identities = 58/120 (48%), Positives = 75/120 (62%), Gaps = 5/120 (4%)

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

Query: 161 PWRQKGTGRARHGTLRGPQFRGGTTMHGPKPRSHAIKLNKKVRRLGLKIALSARAAEGKV 220
            W QK TGRARHG +  P F GG  + GPKPR ++  L KKVR+ GL +A++ RA EGK+
Sbjct: 64  IWPQKHTGRARHGDIGAPIFVGGGVVFGPKPRDYSYTLPKKVRKKGLAMAVADRAREGKL 123


>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 = 25.4 bits (56), Expect = 5.6
 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    0.394 

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: 890,658
Number of extensions: 39772
Number of successful extensions: 83
Number of sequences better than 10.0: 1
Number of HSP's gapped: 81
Number of HSP's successfully gapped: 7
Length of query: 251
Length of database: 2,407,596
Length adjustment: 83
Effective length of query: 168
Effective length of database: 1,268,006
Effective search space: 213025008
Effective search space used: 213025008
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: 52 (24.3 bits)