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)