RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2472
         (571 letters)



>d1gzga_ c.1.10.3 (A:) 5-aminolaevulinate dehydratase, ALAD
           (porphobilinogen synthase) {Pseudomonas aeruginosa
           [TaxId: 287]}
          Length = 329

 Score = 28.4 bits (63), Expect = 2.3
 Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 10/49 (20%)

Query: 57  RGYCTRRIRRLRKTLHLPQGDKRHFKKREVTEQHLKDEKFIYIPLMLAE 105
           R Y   R+RR R+             +R V E  L  +  I  P+ + +
Sbjct: 2   RAYPYTRLRRNRRDDFS---------RRLVRENVLTVDDLIL-PVFVLD 40


>d2gy9d1 d.66.1.2 (D:2-205) Ribosomal protein S4 {Escherichia coli
          [TaxId: 562]}
          Length = 204

 Score = 27.9 bits (62), Expect = 2.3
 Identities = 9/30 (30%), Positives = 11/30 (36%)

Query: 55 RYRGYCTRRIRRLRKTLHLPQGDKRHFKKR 84
          RY G   +  RR    L L  G +    K 
Sbjct: 1  RYLGPKLKLSRREGTDLFLKSGVRAIDTKC 30


>d2j0181 d.301.1.1 (8:2-65) Ribosomal protein L35p {Thermus
          thermophilus [TaxId: 274]}
          Length = 64

 Score = 25.8 bits (57), Expect = 2.8
 Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 4/41 (9%)

Query: 43 QQQHGLRHGDYQRYRGYCTRRIRRLRKTLHLPQGDKRHFKK 83
            + G RH ++Q+      + IR+  +   L + +    K 
Sbjct: 23 AMKTGKRHLNWQK----SGKEIRQKGRKFVLAKPEAERIKL 59


>d1oywa1 a.4.5.43 (A:407-516) DNA helicase RecQ DNA-binding domain
           {Escherichia coli [TaxId: 562]}
          Length = 110

 Score = 26.7 bits (59), Expect = 3.5
 Identities = 15/83 (18%), Positives = 23/83 (27%), Gaps = 11/83 (13%)

Query: 35  ILKIIKDAQQQHGLRH-GDYQRYRGYCTRRIRRLRKTLHLPQGDKRHFKKRE-------- 85
            L  I    Q+ G+ +  +    RG   +RIR          G  R              
Sbjct: 13  ALSTIGRVNQRFGMGYVVEV--IRGANNQRIRDYGHDKLKVYGMGRDKSHEHWVSVIRQL 70

Query: 86  VTEQHLKDEKFIYIPLMLAERAW 108
           +    +      +  L L E A 
Sbjct: 71  IHLGLVTQNIAQHSALQLTEAAR 93


>d1o5xa_ c.1.1.1 (A:) Triosephosphate isomerase {Plasmodium
           falciparum [TaxId: 5833]}
          Length = 246

 Score = 27.1 bits (59), Expect = 5.2
 Identities = 12/97 (12%), Positives = 33/97 (34%), Gaps = 5/97 (5%)

Query: 5   GNIAENEDNAVKVQPKETPAAKPKVVYT-----IEILKIIKDAQQQHGLRHGDYQRYRGY 59
           G +   +         +   +K  VV        +  + +  ++   G+++        Y
Sbjct: 13  GTLESIKSLTNSFNNLDFDPSKLDVVVFPVSVHYDHTRKLLQSKFSTGIQNVSKFGNGSY 72

Query: 60  CTRRIRRLRKTLHLPQGDKRHFKKREVTEQHLKDEKF 96
                  + K L++      HF++R+   +  +D + 
Sbjct: 73  TGEVSAEIAKDLNIEYVIIGHFERRKYFHETDEDVRE 109


>gi|94984680|ref|YP_604044.1|(2-62:67) 50S ribosomal protein L35
          [Deinococcus geothermalis DSM 11300] 
          gi|145572732|sp|Q1J0V9.1|RL35_DEIGD RecName: Full=50S
          ribosomal protein L35   gi|94554961|gb|ABF44875.1|
          ribosomal protein L35 [Deinococcus geothermalis DSM
          11300]  E=4e-21 s/c=1.69 id=84% cov=98%
          Length = 61

 Score = 25.0 bits (55), Expect = 5.6
 Identities = 8/40 (20%), Positives = 13/40 (32%), Gaps = 4/40 (10%)

Query: 44 QQHGLRHGDYQRYRGYCTRRIRRLRKTLHLPQGDKRHFKK 83
           + G RH +  +        IR   K   L + +    K 
Sbjct: 24 FKSGKRHQNTGK----SGDEIRGKGKGFVLAKSEWARMKL 59


>d2qam31 d.301.1.1 (3:1-64) Ribosomal protein L35p {Escherichia
          coli [TaxId: 562]}
          Length = 64

 Score = 25.0 bits (55), Expect = 5.8
 Identities = 7/23 (30%), Positives = 10/23 (43%)

Query: 61 TRRIRRLRKTLHLPQGDKRHFKK 83
          T+R R LR    + +GD      
Sbjct: 37 TKRKRHLRPKAMVSKGDLGLVIA 59


>d1u3da2 c.28.1.1 (A:13-197) Cryptochrome {Thale cress (Arabidopsis
           thaliana) [TaxId: 3702]}
          Length = 185

 Score = 26.9 bits (58), Expect = 6.2
 Identities = 14/58 (24%), Positives = 18/58 (31%), Gaps = 3/58 (5%)

Query: 507 DTEPGTVAKPGAKLKKV--PLAERLGEYYEDPSLASKSPNVIKLPPDMQPIPAKPLFF 562
             EP  V     +   +     ER      DP      P  I +  D+    A PL F
Sbjct: 129 LYEPWEVTDELGRPFSMFAAFWERCLSMPYDPESPLLPPKKI-ISGDVSKCVADPLVF 185


>d2uubd1 d.66.1.2 (D:2-209) Ribosomal protein S4 {Thermus
          thermophilus [TaxId: 274]}
          Length = 208

 Score = 26.8 bits (59), Expect = 6.5
 Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 4/34 (11%)

Query: 55 RYRGYCTRRIRRLRKTLHLP----QGDKRHFKKR 84
          RY G   R  RR    L+L        K   ++R
Sbjct: 2  RYIGPVCRLCRREGVKLYLKGERCYSPKCAMERR 35


>d1ooaa2 b.2.5.3 (A:38-250) p50 subunit of NF-kappa B (NFKB),
           N-terminal domain {Mouse (Mus musculus) [TaxId: 10090]}
          Length = 213

 Score = 26.4 bits (58), Expect = 7.6
 Identities = 10/67 (14%), Positives = 14/67 (20%)

Query: 57  RGYCTRRIRRLRKTLHLPQGDKRHFKKREVTEQHLKDEKFIYIPLMLAERAWGYAMQLRQ 116
            G CT         +        H  K++V E          I            +   Q
Sbjct: 81  DGVCTVTAGPKDMVVGFANLGILHVTKKKVFETLEARMTEACIRGYNPGLLVHSDLAYLQ 140

Query: 117 EANTEPR 123
                 R
Sbjct: 141 AEGGGDR 147


  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
   0.316    0.131    0.368 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,990,186
Number of extensions: 92141
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 251
Number of HSP's successfully gapped: 17
Length of query: 571
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 481
Effective length of database: 1,171,896
Effective search space: 563681976
Effective search space used: 563681976
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: 55 (25.0 bits)