RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 026552
         (237 letters)



>d1io2a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
           Thermococcus kodakaraensis [TaxId: 311400]}
          Length = 213

 Score = 69.4 bits (169), Expect = 4e-15
 Identities = 43/128 (33%), Positives = 65/128 (50%), Gaps = 8/128 (6%)

Query: 42  ISHDSAIGLITRVLNIGILLTEVYLDTVG-DAEKYQAKLSQRFPSIKFVVSK-KADSLYP 99
           ++          + ++ +    +Y D    D E++  +L +R      VV+K KAD ++P
Sbjct: 80  LNEFEVENFAKALNSLKVKPDVIYADAADVDEERFARELGERLNFEAEVVAKHKADDIFP 139

Query: 100 VVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSL 159
           VVS ASI+AKVTRDR +     E      +   GSGYP DP T+A+L ++      FP +
Sbjct: 140 VVSAASILAKVTRDRAVEKLKEE------YGEIGSGYPSDPRTRAFLENYYREHGEFPPI 193

Query: 160 VRFSWGTC 167
           VR  W T 
Sbjct: 194 VRKGWKTL 201


>d1ekea_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
           Methanococcus jannaschii [TaxId: 2190]}
          Length = 225

 Score = 65.3 bits (158), Expect = 2e-13
 Identities = 34/95 (35%), Positives = 52/95 (54%), Gaps = 6/95 (6%)

Query: 73  EKYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNF 132
           +K +  + +R  +IK +   KAD+ YPVVS ASI+AK  RD  +  +      + ++ + 
Sbjct: 127 DKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYY------KKIYGDI 180

Query: 133 GSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
           GSGYP DP+T  +L D+       P + R  W TC
Sbjct: 181 GSGYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTC 215


>d1uaxa_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
           Pyrococcus horikoshii [TaxId: 53953]}
          Length = 211

 Score = 62.6 bits (151), Expect = 1e-12
 Identities = 47/167 (28%), Positives = 76/167 (45%), Gaps = 16/167 (9%)

Query: 3   SEAALPKWASNPFGWAVDIIDPRELSAKMLNKNKINLNEISHDSAIGLITRVLNIGILLT 62
            E    K       + V ++ P+E+  +  + N++   +            + ++ I   
Sbjct: 49  REKLFSKLIDILDDYYVLLVTPKEIDERHHSMNELEAEKFVV--------ALNSLRIKPQ 100

Query: 63  EVYLDTVGDAEKYQAKLSQRFPSIKFVVS--KKADSLYPVVSGASIVAKVTRDRTLRGWI 120
           ++Y+D+     K  A L +     +  V    KAD+ Y +VS ASI+AKVTRDR +    
Sbjct: 101 KIYVDSADVDPKRFASLIKAGLKYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKL- 159

Query: 121 FEETAENMHRNFGSGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
                +  +  FGSGYP DP TK WL ++      FP +VR +W T 
Sbjct: 160 -----KQKYGEFGSGYPSDPRTKEWLEEYYKQYGDFPPIVRRTWETA 201


>d1i39a_ c.55.3.1 (A:) Class II ribonuclease H (RNase HII) {Archaeon
           Archaeoglobus fulgidus [TaxId: 2234]}
          Length = 200

 Score = 56.8 bits (136), Expect = 1e-10
 Identities = 30/94 (31%), Positives = 45/94 (47%), Gaps = 7/94 (7%)

Query: 74  KYQAKLSQRFPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFG 133
           +  ++  +    ++ V   KAD  YP+V+ ASI+AKV R+R +         +    +FG
Sbjct: 108 ERLSRELEEITGLRVVAEHKADEKYPLVAAASIIAKVEREREIERL------KEKFGDFG 161

Query: 134 SGYPGDPETKAWLTDHKHIIFGFPSLVRFSWGTC 167
           SGY  DP T+  L +        PS VR  W T 
Sbjct: 162 SGYASDPRTREVLKEWIA-SGRIPSCVRMRWKTV 194


>d2etja1 c.55.3.1 (A:1-221) Class II ribonuclease H (RNase HII)
           {Thermotoga maritima [TaxId: 2336]}
          Length = 221

 Score = 54.3 bits (130), Expect = 1e-09
 Identities = 23/118 (19%), Positives = 39/118 (33%), Gaps = 9/118 (7%)

Query: 83  FPSIKFVVSKKADSLYPVVSGASIVAKVTRDRTLRGWIFEETAENMHRNFGSGYPGDPET 142
             S+      K D    ++  ASIVAKV RDR +  +       + H++   GY      
Sbjct: 112 ELSVPGTCLVKGDQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKH--KGYATKEHL 169

Query: 143 KAWLTDHKHIIFGFPSLVRFSWGTCTSHF-KDIVEVLWESDEMDEDVSSRRSGKRQLK 199
                       G   + R S+         D++   +E   + E+   R       +
Sbjct: 170 NEIRK------NGVLPIHRLSFEPVLELLTDDLLREFFEKGLISENRFERILNLLGAR 221


  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
   0.317    0.133    0.396 

Gapped
Lambda     K      H
   0.267   0.0646    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 891,904
Number of extensions: 40022
Number of successful extensions: 77
Number of sequences better than 10.0: 1
Number of HSP's gapped: 73
Number of HSP's successfully gapped: 9
Length of query: 237
Length of database: 2,407,596
Length adjustment: 83
Effective length of query: 154
Effective length of database: 1,268,006
Effective search space: 195272924
Effective search space used: 195272924
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 (21.7 bits)
S2: 51 (23.6 bits)