RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6779
         (144 letters)



>d1ipaa2 d.79.3.3 (A:1-105) RrmA (RrmH), N-terminal domain {Thermus
           thermophilus [TaxId: 274]}
          Length = 105

 Score = 60.8 bits (147), Expect = 1e-13
 Identities = 17/86 (19%), Positives = 34/86 (39%), Gaps = 7/86 (8%)

Query: 5   KSRKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQ-------WDILKELPLPEDVPQH 57
             RK R+ +   ++EG R +  AL+A ++L+     +         +   L     +   
Sbjct: 18  LERKHRDSQRRFLIEGAREIERALQAGIELEQALVWEGGLNPEEQQVYAALGRVGRLALL 77

Query: 58  RVDYKNIQLWSDLVTPPGIIGIFELP 83
            V    ++  S    P G+I +  +P
Sbjct: 78  EVSEAVLKKLSVRDNPAGLIALARMP 103


>d1mxia_ c.116.1.1 (A:) Hypothetical tRNA/rRNA methyltransfease
           HI0766 (YibK homologue) {Haemophilus influenzae [TaxId:
           727]}
          Length = 156

 Score = 48.7 bits (115), Expect = 1e-08
 Identities = 14/48 (29%), Positives = 22/48 (45%)

Query: 97  LNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
           L+IV      P N G+I+R+CA  G R  +         D ++ R+  
Sbjct: 2   LDIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGL 49


>d1gz0a1 c.116.1.1 (A:78-243) RlmB, C-terminal domain {Escherichia
           coli [TaxId: 562]}
          Length = 166

 Score = 46.0 bits (108), Expect = 1e-07
 Identities = 11/47 (23%), Positives = 20/47 (42%)

Query: 96  PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRA 142
           P  ++ D + DP N+G+ LR   A G   V+  +      +    + 
Sbjct: 18  PFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKV 64


>d1v2xa_ c.116.1.1 (A:) tRNA (Gm18) methyltransferase TrmH {Thermus
           thermophilus [TaxId: 274]}
          Length = 191

 Score = 44.2 bits (103), Expect = 7e-07
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 96  PLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
            L ++ +N+  P N+ +ILR C AVG  +         +         +
Sbjct: 22  DLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGS 70


>d1ipaa1 c.116.1.1 (A:106-263) RrmA (RrmH), C-terminal domain
           {Thermus thermophilus [TaxId: 274]}
          Length = 158

 Score = 43.8 bits (102), Expect = 7e-07
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 87  IASIDPASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGC 131
           +    P+   L +V   +  PGN+G++LR   A GA  V+ + G 
Sbjct: 2   LEEYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGV 46


>d1no7a_ e.48.1.1 (A:) Major capsid protein VP5 {Herpes simplex
           virus 1 [TaxId: 10298]}
          Length = 562

 Score = 29.8 bits (67), Expect = 0.11
 Identities = 10/56 (17%), Positives = 21/56 (37%)

Query: 59  VDYKNIQLWSDLVTPPGIIGIFELPAHPIASIDPASLPLNIVCDNIRDPGNMGSIL 114
           V +  +      +  P I    E P+ P+        P N+V + +    + G ++
Sbjct: 347 VRFDRVYATLQNMVVPEIAPGEECPSDPVTDPAHPLHPANLVANTVNAMFHNGRVV 402


>d2qalr1 a.4.8.1 (R:19-73) Ribosomal protein S18 {Escherichia coli
          [TaxId: 562]}
          Length = 55

 Score = 24.1 bits (53), Expect = 2.0
 Identities = 7/19 (36%), Positives = 11/19 (57%)

Query: 59 VDYKNIQLWSDLVTPPGII 77
          +DYK+I    + +T  G I
Sbjct: 2  IDYKDIATLKNYITESGKI 20


>d2e7ya1 d.157.1.7 (A:1-280) Ribonuclease Z (RNase Z) {Thermotoga
          maritima [TaxId: 2336]}
          Length = 280

 Score = 25.5 bits (54), Expect = 3.0
 Identities = 15/76 (19%), Positives = 23/76 (30%), Gaps = 8/76 (10%)

Query: 15 WLMLEGKRILIDA--------LKANLKLKMVFFSQWDILKELPLPEDVPQHRVDYKNIQL 66
          W+    +RIL DA               K VF +   +     L   V        + + 
Sbjct: 14 WIYYSPERILFDAGEGVSTTLGSKVYAFKYVFLTHGHVDHIAGLWGVVNIRNNGMGDREK 73

Query: 67 WSDLVTPPGIIGIFEL 82
            D+  P G   + E 
Sbjct: 74 PLDVFYPEGNRAVEEY 89


>d2uubr1 a.4.8.1 (R:19-88) Ribosomal protein S18 {Thermus
          thermophilus [TaxId: 274]}
          Length = 70

 Score = 23.8 bits (52), Expect = 4.0
 Identities = 5/19 (26%), Positives = 11/19 (57%)

Query: 59 VDYKNIQLWSDLVTPPGII 77
           DY+N+++    ++  G I
Sbjct: 14 RDYRNVEVLKRFLSETGKI 32


  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
   0.324    0.141    0.438 

Gapped
Lambda     K      H
   0.267   0.0717    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 588,118
Number of extensions: 27561
Number of successful extensions: 71
Number of sequences better than 10.0: 1
Number of HSP's gapped: 70
Number of HSP's successfully gapped: 10
Length of query: 144
Length of database: 2,407,596
Length adjustment: 77
Effective length of query: 67
Effective length of database: 1,350,386
Effective search space: 90475862
Effective search space used: 90475862
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 49 (22.7 bits)