RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254781076|ref|YP_003065489.1| ribonuclease HII [Candidatus
Liberibacter asiaticus str. psy62]
         (209 letters)



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

 Score =  180 bits (458), Expect = 7e-47
 Identities = 87/188 (46%), Positives = 114/188 (60%), Gaps = 4/188 (2%)

Query: 20  EKNMWPVAGIDEVGRGALAGPVVVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSA 79
           +K    VAG+DE GRG LAGPVV AA++L+      GINDSK++S  KRE L ++I   A
Sbjct: 8   KKEFGIVAGVDEAGRGCLAGPVVAAAVVLEKEIE--GINDSKQLSPAKRERLLDEIMEKA 65

Query: 80  IISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQAFAVIKG 139
            + I  AS + ID +NI  AT  A+  A+ENL V P   L+DG+ I   +P     ++KG
Sbjct: 66  AVGIGIASPEEIDLYNIFNATKLAMNRALENLSVKPSFVLVDGKGIELSVPGTC--LVKG 123

Query: 140 DSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGPSCIHRL 199
           D  S  I AASI+AKV RDRLM   H+ YP + F  H GY T +H   I++ G   IHRL
Sbjct: 124 DQKSKLIGAASIVAKVFRDRLMSEFHRMYPQFSFHKHKGYATKEHLNEIRKNGVLPIHRL 183

Query: 200 TFRPLRNL 207
           +F P+  L
Sbjct: 184 SFEPVLEL 191


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

 Score =  146 bits (370), Expect = 1e-36
 Identities = 55/206 (26%), Positives = 97/206 (47%), Gaps = 28/206 (13%)

Query: 26  VAGIDEVGRGALAGPVVVAAIILDPNNIP----FGINDSKKISHKKREELYEKITSSAII 81
           +AGIDE GRG + GP+V+AA+++D N++P      + DSKK++ K+RE+L+ +I      
Sbjct: 3   IAGIDEAGRGPVIGPMVIAAVVVDENSLPKLEELKVRDSKKLTPKRREKLFNEILGVLDD 62

Query: 82  SI---SSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPED---------- 128
            +            +  +++  ++    A+ +L+V P     D   + E+          
Sbjct: 63  YVILELPPDVIGSREGTLNEFEVENFAKALNSLKVKPDVIYADAADVDEERFARELGERL 122

Query: 129 -LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQV 187
               +  A  K D I   ++AASI+AKVTRDR +    ++Y + G     GYP+    + 
Sbjct: 123 NFEAEVVAKHKADDIFPVVSAASILAKVTRDRAVEKLKEEYGEIGS----GYPSDPRTRA 178

Query: 188 IKEK------GPSCIHRLTFRPLRNL 207
             E           I R  ++ L+ +
Sbjct: 179 FLENYYREHGEFPPIVRKGWKTLKKI 204


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

 Score =  133 bits (335), Expect = 1e-32
 Identities = 52/202 (25%), Positives = 94/202 (46%), Gaps = 20/202 (9%)

Query: 26  VAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSA-- 79
           VAG+DE GRG + GP+V+   ++D  NI      G+ DSK+++  +RE+L+ K+      
Sbjct: 3   VAGVDEAGRGPVIGPLVIGVAVIDEKNIERLRDIGVKDSKQLTPGQREKLFSKLIDILDD 62

Query: 80  -IISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPED---------- 128
             + + +        H++++   +    A+ +L++ P+   +D   +             
Sbjct: 63  YYVLLVTPKEIDERHHSMNELEAEKFVVALNSLRIKPQKIYVDSADVDPKRFASLIKAGL 122

Query: 129 -LPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKH-QQ 186
                  A  K D+    ++AASIIAKVTRDR +    +KY ++G        T +  ++
Sbjct: 123 KYEATVIAEHKADAKYEIVSAASIIAKVTRDREIEKLKQKYGEFGSGYPSDPRTKEWLEE 182

Query: 187 VIKEKGPSC-IHRLTFRPLRNL 207
             K+ G    I R T+   R +
Sbjct: 183 YYKQYGDFPPIVRRTWETARKI 204


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

 Score =  121 bits (304), Expect = 4e-29
 Identities = 49/195 (25%), Positives = 80/195 (41%), Gaps = 14/195 (7%)

Query: 27  AGIDEVGRGALAGPVVVAAIILDPNNI--PFGINDSKKISHKKREELYE----------- 73
           AGIDE G+G + GP+VVA +     +     G+ DSKK+S  +REEL E           
Sbjct: 3   AGIDEAGKGCVIGPLVVAGVACSDEDRLRKLGVKDSKKLSQGRREELAEEIRKICRTEVL 62

Query: 74  KITSSAIISISSASHQYIDKHNIHKATLDAIYHAVENLQVIPRSALIDGRSIPEDLPCQA 133
           K++   +    +A          +   +  +   +  +           R + E    + 
Sbjct: 63  KVSPENLDERMAAKTINEILKECYAEIILRLKPEIAYVDSPDVIPERLSRELEEITGLRV 122

Query: 134 FAVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGFDSHVGYPTAKHQQVIKEKGP 193
            A  K D     +AAASIIAKV R+R +    +K+ D+G        T +  +     G 
Sbjct: 123 VAEHKADEKYPLVAAASIIAKVEREREIERLKEKFGDFGSGYASDPRTREVLKEWIASGR 182

Query: 194 SC-IHRLTFRPLRNL 207
                R+ ++ + NL
Sbjct: 183 IPSCVRMRWKTVSNL 197


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

 Score =  121 bits (304), Expect = 4e-29
 Identities = 48/220 (21%), Positives = 80/220 (36%), Gaps = 42/220 (19%)

Query: 26  VAGIDEVGRGALAGPVVVAAIILDPNNIPF----GINDSKKISHKKREELYEKITSSAII 81
           + GIDE GRG + GP+VV A  ++          G+ DSK+++  KR  L + + +   +
Sbjct: 3   IIGIDEAGRGPVLGPMVVCAFAIEKEREEELKKLGVKDSKELTKNKRAYLKKLLENLGYV 62

Query: 82  SISSASHQY-------------------------IDKHNIHKATLDAIYHAVENLQVIPR 116
                  +                          I+K NI    ++    A         
Sbjct: 63  EKRILEAEEINQLMNSINLNDIEINAFSKVAKNLIEKLNIRDDEIEIYIDACSTNTKKFE 122

Query: 117 SALIDGRSIPEDLPCQAF---AVIKGDSISLSIAAASIIAKVTRDRLMRIAHKKYPDYGF 173
            +  D                A  K D+    ++AASIIAK  RD ++    K Y D G 
Sbjct: 123 DSFKDKIEDIIKERNLNIKIIAEHKADAKYPVVSAASIIAKAERDEIIDYYKKIYGDIGS 182

Query: 174 DSHVGYPT-AKHQQVIKE-----KGPSCIHRLTFRPLRNL 207
               GYP+  K  + +++     K    I R  ++  + +
Sbjct: 183 ----GYPSDPKTIKFLEDYFKKHKKLPDIARTHWKTCKRI 218


>d1oaoa_ e.26.1.2 (A:) Bifunctional carbon monoxide
           dehydrogenase/acetyl-CoA synthase (CODH/ACS) beta (CODH)
           subunit {Moorella thermoacetica [TaxId: 1525]}
          Length = 673

 Score = 26.0 bits (57), Expect = 2.6
 Identities = 14/68 (20%), Positives = 25/68 (36%), Gaps = 6/68 (8%)

Query: 43  VAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLD 102
           + A+ +D   I   I+   +  H +       IT++    I  A H         ++   
Sbjct: 345 IDAMCVDVQCIMPSISAVAECYHTRI------ITTADNAKIPGAYHIDYQTATAIESAKT 398

Query: 103 AIYHAVEN 110
           AI  A+E 
Sbjct: 399 AIRMAIEA 406


>d2dt5a2 c.2.1.12 (A:78-203) Transcriptional repressor Rex,
          C-terminal domain {Thermus aquaticus [TaxId: 271]}
          Length = 126

 Score = 25.9 bits (57), Expect = 2.8
 Identities = 4/50 (8%), Positives = 14/50 (28%)

Query: 42 VVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYI 91
          +     +DP  +   +            +        A++++   + Q  
Sbjct: 30 LRGFFDVDPEKVGRPVRGGVIEHVDLLPQRVPGRIEIALLTVPREAAQKA 79


>d1su7a_ e.26.1.2 (A:) Ni-containing carbon monoxide dehydrogenase
           {Carboxydothermus hydrogenoformans [TaxId: 129958]}
          Length = 633

 Score = 25.2 bits (55), Expect = 4.0
 Identities = 11/69 (15%), Positives = 25/69 (36%), Gaps = 6/69 (8%)

Query: 42  VVAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATL 101
            + A+ILD   I   +    + +          IT+  +  I+ A+H    +    +   
Sbjct: 320 ALDAMILDYQCIQPSVATIAECTGTTV------ITTMEMSKITGATHVNFAEEAAVENAK 373

Query: 102 DAIYHAVEN 110
             +  A++ 
Sbjct: 374 QILRLAIDT 382


>d1t64a_ c.42.1.2 (A:) Histone deacetylase 8, HDAC8 {Human (Homo
           sapiens) [TaxId: 9606]}
          Length = 364

 Score = 24.4 bits (52), Expect = 7.9
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 5/59 (8%)

Query: 110 NLQVIPRS-----ALIDGRSIPEDLPCQAFAVIKGDSISLSIAAASIIAKVTRDRLMRI 163
           NL    R       +I G+++  ++P   F    G    L I  +    +    R+ +I
Sbjct: 294 NLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQI 352


>d1jqka_ e.26.1.2 (A:) Ni-containing carbon monoxide dehydrogenase
           {Rhodospirillum rubrum [TaxId: 1085]}
          Length = 610

 Score = 24.1 bits (52), Expect = 9.4
 Identities = 14/68 (20%), Positives = 26/68 (38%), Gaps = 6/68 (8%)

Query: 43  VAAIILDPNNIPFGINDSKKISHKKREELYEKITSSAIISISSASHQYIDKHNIHKATLD 102
           + A+++D   I   +    +  H +       IT+     IS A+H   D+H   +    
Sbjct: 302 LEAMVVDVQCIMPSLPRIAECFHTQI------ITTDKHNKISGATHVPFDEHKAVETAKT 355

Query: 103 AIYHAVEN 110
            I  A+  
Sbjct: 356 IIRMAIAA 363


  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    0.397 

Gapped
Lambda     K      H
   0.267   0.0656    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 789,679
Number of extensions: 35767
Number of successful extensions: 109
Number of sequences better than 10.0: 1
Number of HSP's gapped: 94
Number of HSP's successfully gapped: 16
Length of query: 209
Length of database: 2,407,596
Length adjustment: 81
Effective length of query: 128
Effective length of database: 1,295,466
Effective search space: 165819648
Effective search space used: 165819648
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: 51 (23.6 bits)