RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 033139
         (126 letters)



>d2uubm1 a.156.1.1 (M:2-126) Ribosomal protein S13 {Thermus
           thermophilus [TaxId: 274]}
          Length = 125

 Score = 71.0 bits (174), Expect = 1e-17
 Identities = 22/105 (20%), Positives = 42/105 (40%), Gaps = 22/105 (20%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
           R+    +   +++  ALT I GIG+  A    +K  ++   R  +L+ AE+ +L      
Sbjct: 2   RIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRL------ 55

Query: 74  PRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118
            R++    W L                  L  ++  +++RL  I 
Sbjct: 56  -REYVENTWKL---------------EGELRAEVAANIKRLMDIG 84


>d2gy9m1 a.156.1.1 (M:1-114) Ribosomal protein S13 {Escherichia coli
           [TaxId: 562]}
          Length = 114

 Score = 70.2 bits (172), Expect = 2e-17
 Identities = 20/105 (19%), Positives = 39/105 (37%), Gaps = 23/105 (21%)

Query: 14  RVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVVVAN 73
           R+   N+   +  + ALTSI G+G+  +  +   A +  + +  ELS  ++D        
Sbjct: 2   RIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDT------- 54

Query: 74  PRQFKIPDWFLNRQKDYKDGRYSQVVSNALDMKLRDDLERLKKIR 118
                            +D     VV   L  ++   ++RL  + 
Sbjct: 55  ----------------LRDEVAKFVVEGDLRREISMSIKRLMDLG 83


>d1iega_ b.57.1.1 (A:) Human cytomegalovirus protease {Human
           cytomegalovirus [TaxId: 10359]}
          Length = 248

 Score = 26.7 bits (59), Expect = 0.75
 Identities = 20/104 (19%), Positives = 44/104 (42%), Gaps = 9/104 (8%)

Query: 18  TNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD-MNKRAGELSAAELDQLMVVVANPRQ 76
           T++ G +   F   ++  +GRR   +     D + + +R  +L+AA+ D L         
Sbjct: 137 TSLSGSETTPFKAVALCSVGRRRGTLAVYGRDPEWVTQRFPDLTAADRDGLRAQWQRCGS 196

Query: 77  FKIP-DWFLNRQKDYKDGRYSQVVSNALD-MKLRDDLERLKKIR 118
             +       R   Y       ++ N++D + +R+ L +L+  +
Sbjct: 197 TAVDASGDPFRSDSYG------LLGNSVDALYIRERLPKLRYDK 234


>d1vdka_ a.127.1.1 (A:) Fumarase {Thermus thermophilus [TaxId: 274]}
          Length = 460

 Score = 26.7 bits (58), Expect = 1.0
 Identities = 14/72 (19%), Positives = 24/72 (33%), Gaps = 14/72 (19%)

Query: 3   LVANEDFQHILRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKAD------VDMNKRA 56
           +  N +       +   +     +  AL   K IG   A  + KKA              
Sbjct: 388 IEPNLE------RIEEYLQKNPMLATALN--KAIGYDKAAEIVKKALKEKKTLKQAALEL 439

Query: 57  GELSAAELDQLM 68
           G L+  E D+++
Sbjct: 440 GYLTEEEFDRIV 451


>d2a1jb1 a.60.2.5 (B:219-296) DNA excision repair protein ERCC-1
          {Human (Homo sapiens) [TaxId: 9606]}
          Length = 78

 Score = 24.1 bits (52), Expect = 2.6
 Identities = 4/27 (14%), Positives = 12/27 (44%)

Query: 21 DGKQKIMFALTSIKGIGRRLANIVCKK 47
          D   ++   LT++K + +  +  +   
Sbjct: 12 DFVSRVTECLTTVKSVNKTDSQTLLTT 38


>d1o6ea_ b.57.1.1 (A:) Epstein-Barr virus protease {Human
           herpesvirus 4 [TaxId: 10376]}
          Length = 232

 Score = 25.1 bits (55), Expect = 2.6
 Identities = 22/109 (20%), Positives = 40/109 (36%), Gaps = 11/109 (10%)

Query: 13  LRVLNTNVDGKQKIMFALTSIKGIGRRLANIVCKKADVD-MNKRAGELSAAELDQLMVVV 71
             +  T  DG +   F   SI  +GRR         D+  + K   +L  +   Q+    
Sbjct: 119 PDIPQTTADGGKLSFFDHVSICALGRRRGTTAVYGTDLAWVLKHFSDLEPSIAAQIENDA 178

Query: 72  ANP-RQFKIPDWFLNRQKDYKDGRYSQVVSNALD-MKLRDDLERLKKIR 118
               R+   P+                +++ A+D   LR+ +E L++ R
Sbjct: 179 NAAKRESGCPEDH---PLPLTK-----LIAKAIDAGFLRNRVETLRQDR 219


>d2bgwa1 a.60.2.5 (A:160-229) DNA repair endonuclease XPF
          {Aeropyrum pernix [TaxId: 56636]}
          Length = 70

 Score = 23.6 bits (51), Expect = 3.3
 Identities = 11/50 (22%), Positives = 20/50 (40%), Gaps = 5/50 (10%)

Query: 21 DGKQKIMFALTSIKGIGRRLANIVCKKADVDMNKRAGELSAAELDQLMVV 70
          D ++  ++ L S  GIGRR A     +  ++          A   ++  V
Sbjct: 6  DVREWQLYILQSFPGIGRRTA-----ERILERFGSLERFFTASKAEISKV 50


>d2pbka1 b.57.1.1 (A:3-230) KSHV protease {Kaposi's
           sarcoma-associated herpesvirus [TaxId: 37296]}
          Length = 228

 Score = 23.9 bits (52), Expect = 6.8
 Identities = 20/94 (21%), Positives = 40/94 (42%), Gaps = 9/94 (9%)

Query: 27  MFALTSIKGIGRRLANIVCKKADVD-MNKRAGELSAAELDQLMVVVANPRQFKIPDWFLN 85
           +F   S+  +GRR   +     D + +  R   +S +E   ++  V++ R   +     N
Sbjct: 129 VFQHVSLCALGRRRGTVAVYGHDAEWVVSRFSSVSKSERAHILQHVSSCRLEDLSTP--N 186

Query: 86  RQKDYKDGRYSQVVSNALD-MKLRDDLERLKKIR 118
                +      +++ A+D   +RD L+ LK  R
Sbjct: 187 FVSPLET-----LMAKAIDAGFIRDRLDLLKTDR 215


  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    0.138    0.389 

Gapped
Lambda     K      H
   0.267   0.0629    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 459,405
Number of extensions: 19339
Number of successful extensions: 79
Number of sequences better than 10.0: 1
Number of HSP's gapped: 79
Number of HSP's successfully gapped: 16
Length of query: 126
Length of database: 2,407,596
Length adjustment: 75
Effective length of query: 51
Effective length of database: 1,377,846
Effective search space: 70270146
Effective search space used: 70270146
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: 41 (22.0 bits)
S2: 48 (22.5 bits)