RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780796|ref|YP_003065209.1| ribonuclease H [Candidatus Liberibacter asiaticus str. psy62] (152 letters) >3h08_A RNH (ribonuclease H); RNAse H, 3D-structure, endonuclease, hydrolase, magnesium, metal-binding; 1.60A {Chlorobaculum tepidum} (A:) Length = 146 Score = 139 bits (351), Expect = 2e-34 Identities = 72/139 (51%), Positives = 95/139 (68%), Gaps = 1/139 (0%) Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67 + YTDGA SGNPG GGWG LL Y K ISG + TTNNRMELMAAIK L ALK P Sbjct: 4 TITIYTDGAASGNPGKGGWGALLMYGSSRKEISGYDPATTNNRMELMAAIKGLEALKEPA 63 Query: 68 KVLLYTDSSYVHKGFSQ-WIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIK 126 +V LY+DS+Y+ ++ W+K+W +NGWKT+ KK V+NIDLW + ++ + H+V + +K Sbjct: 64 RVQLYSDSAYLVNAMNEGWLKRWVKNGWKTAAKKPVENIDLWQEILKLTTLHRVTFHKVK 123 Query: 127 GHAGNQENEKVDRIARNAA 145 GH+ N N + D +AR A Sbjct: 124 GHSDNPYNSRADELARLAI 142 >2e4l_A Ribonuclease HI, RNAse HI; hydrolase, endoribonuclease; 2.00A {Shewanella oneidensis mr-1} PDB: 2zqb_A (A:) Length = 158 Score = 130 bits (327), Expect = 1e-31 Identities = 72/137 (52%), Positives = 101/137 (73%) Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68 +H +TDG+C GNPGPGG+G+++ YKG K +S G TTNNRMEL+A I AL ALK PCK Sbjct: 7 IHIFTDGSCLGNPGPGGYGIVMNYKGHTKEMSDGFSLTTNNRMELLAPIVALEALKEPCK 66 Query: 69 VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128 ++L +DS Y+ +G WI W++ GW TS++ VKN+DLW + +A+ H++D W+KGH Sbjct: 67 IILTSDSQYMRQGIMTWIHGWKKKGWMTSNRTPVKNVDLWKRLDKAAQLHQIDWRWVKGH 126 Query: 129 AGNQENEKVDRIARNAA 145 AG+ ENE+ D++AR AA Sbjct: 127 AGHAENERCDQLARAAA 143 >1jl1_A Ribonuclease HI; RNAse HI, protein stability, thermostability, hydrogen exchange, cooperativity, hydrolase; 1.30A {Escherichia coli} (A:) Length = 155 Score = 128 bits (322), Expect = 3e-31 Identities = 78/138 (56%), Positives = 100/138 (72%) Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67 +V +T G+ GNPGPGG+G +LRY+G+EK S G TTNNRMELMAAI AL ALK Sbjct: 4 QVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEHA 63 Query: 68 KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKG 127 +V+L TDS YV +G +QWI W++ GWKT+DKK VKN+DLW + A QH++ W+KG Sbjct: 64 EVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVKG 123 Query: 128 HAGNQENEKVDRIARNAA 145 HAG+ ENE+ D +AR AA Sbjct: 124 HAGHPENERADELARAAA 141 >1ril_A Ribonuclease H; hydrolase(endoribonuclease); 2.80A {Thermus thermophilus} (A:) Length = 166 Score = 120 bits (301), Expect = 1e-28 Identities = 79/146 (54%), Positives = 104/146 (71%), Gaps = 1/146 (0%) Query: 1 MDSKHLREVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKAL 60 M+ + V +TDGAC GNPGPGGW LLR+ EK++SGGE TTNNRMEL AAI+ L Sbjct: 1 MNPSPRKRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGL 60 Query: 61 TALKYPCKVLLYTDSSYVHKGFSQ-WIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHK 119 ALK PC+V LYTDS Y+ K F++ W++ W++ GW+T++ K VKN DLW + A A H+ Sbjct: 61 KALKEPCEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHR 120 Query: 120 VDLYWIKGHAGNQENEKVDRIARNAA 145 V +++KGH G+ ENE+VDR AR A Sbjct: 121 VRFHFVKGHTGHPENERVDREARRQA 146 >1zbf_A Ribonuclease H-related protein; RNAse H, RNA/DNA hybrid, DDE motif, hydrolase; 1.50A {Bacillus halodurans c-125} (A:) Length = 142 Score = 119 bits (298), Expect = 2e-28 Identities = 24/143 (16%), Positives = 46/143 (32%), Gaps = 5/143 (3%) Query: 1 MDSKHLREVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKAL 60 M + + D GNPG + + G+ TNN E +A + L Sbjct: 4 MAKEEIIWESLSVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGL 63 Query: 61 -TALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHK 119 + + +Y++S +W+K + +++T L + E H Sbjct: 64 RYLKERNSRKPIYSNSQTAI----KWVKDKKAKSTLVRNEETALIWKLVDEAEEWLNTHT 119 Query: 120 VDLYWIKGHAGNQENEKVDRIAR 142 + +K K D + Sbjct: 120 YETPILKWQTDKWGEIKADYGRK 142 >2qkb_A Ribonuclease H1, HS-RNAse HC, RNAse H1; RNA/DNA hybrid; 2.40A {Homo sapiens} PDB: 2qk9_A 2qkk_A* (A:) Length = 154 Score = 105 bits (263), Expect = 2e-24 Identities = 47/142 (33%), Positives = 70/142 (49%), Gaps = 5/142 (3%) Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGG---EKETTNNRMELMAAIKALTALKY 65 V YTDG CS N + Y G ++ G TN R E+ AA KA+ K Sbjct: 8 VVVYTDGCCSSNGRRRPRAGIGVYWGPGHPLNVGIRLPGRQTNQRAEIHAACKAIEQAKT 67 Query: 66 PC--KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLY 123 K++LYT+S + G + W++ W++NGWKTS K V N + ++ + + Sbjct: 68 QNINKLVLYTNSXFTINGITNWVQGWKKNGWKTSAGKEVINKEDFVALERLTQGXDIQWX 127 Query: 124 WIKGHAGNQENEKVDRIARNAA 145 + GH+G NE+ DR+AR A Sbjct: 128 HVPGHSGFIGNEEADRLAREGA 149 >2hb5_A Reverse transcriptase/ribonuclease H; RNAse H, hydrolase; 1.59A {Moloney murine leukemia virus} (A:) Length = 164 Score = 100 bits (249), Expect = 1e-22 Identities = 27/143 (18%), Positives = 47/143 (32%), Gaps = 16/143 (11%) Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67 + YTDG+ G G + + + T+ R EL+A +AL + Sbjct: 22 DHTWYTDGSSLLQEGQRKAGAAVTTETEVIWAKALPAGTSAQRAELIALTQALKXAE-GK 80 Query: 68 KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKG 127 K+ +YTDS Y + + ++ ++ + G Sbjct: 81 KLNVYTDSRYAFATAHLTSEGKEIKNKD----------EILALLKALFLPKRLSIIHCPG 130 Query: 128 HAGN-----QENEKVDRIARNAA 145 H + N D+ AR AA Sbjct: 131 HQKGHSAEARGNRXADQAARKAA 153 >1mu2_A HIV-2 RT; HIV-2 reverse transcriptase, AIDS, polymerase, drug design, transferase; 2.35A {Human immunodeficiency virus 2} (A:427-555) Length = 129 Score = 76.9 bits (188), Expect = 1e-15 Identities = 26/136 (19%), Positives = 44/136 (32%), Gaps = 18/136 (13%) Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68 YTDG+C+ G G + + +TTN + EL A + K Sbjct: 11 ETFYTDGSCNRQSKEGKAGYVTDRGKDKVKKLE---QTTNQQAELEAFA--MALTDSGPK 65 Query: 69 VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128 V + DS YV + + + E + + + W+ H Sbjct: 66 VNIIVDSQYVMGIVASQPTESESKIV-------------NQIIEEMIKKEAIYVAWVPAH 112 Query: 129 AGNQENEKVDRIARNA 144 G N++VD + Sbjct: 113 KGIGGNQEVDHLVSQG 128 >2ehg_A Ribonuclease HI; RNAse HI, hyperthermophilic archaeon, double-stranded RNA-dependent RNAse, hydrolase; 1.60A {Sulfolobus tokodaii str} (A:) Length = 149 Score = 74.5 bits (182), Expect = 7e-15 Identities = 32/144 (22%), Positives = 54/144 (37%), Gaps = 20/144 (13%) Query: 9 VHAYTDGACS-GNPG-PGGWGVLLRYKGKEKI-----ISGGEKETTNNRMELMAAIKALT 61 + Y DG C NPG +G ++ ++ +TNN E I + Sbjct: 2 IIGYFDGLCEPKNPGGIATFGFVIYLDNRKIEGYGLAEKPFSINSTNNVAEYSGLICLM- 60 Query: 62 ALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVD 121 +L SS + KG SQ + K +K K+ + + + E + Sbjct: 61 -----ETMLRLGISSPIIKGDSQLVIKQMNGEYKVKAKRIIPLYEKAI---ELKKKLNAT 112 Query: 122 LYWIKGHAGNQENEKVDRIARNAA 145 L W+ EN++ DR++R A Sbjct: 113 LIWVPRE----ENKEADRLSRVAY 132 >3hyf_A Reverse transcriptase/rnaseh; HIV-1, hydrolase, DI-valent metal nucleic acid cleavage mechanism, DI-valent metal coordination; HET: ON1; 1.70A {Human immunodeficiency virus 1} PDB: 1o1w_A 1hrh_A 1rdh_A (A:) Length = 150 Score = 71.6 bits (174), Expect = 5e-14 Identities = 44/139 (31%), Positives = 65/139 (46%), Gaps = 6/139 (4%) Query: 8 EVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPC 67 Y DGA + G G + ++ + +TTN + EL A L Sbjct: 12 AETFYVDGAANRETKLGKAGYVTNRGRQKVV---TLTDTTNQKTELQAIY--LALQDSGL 66 Query: 68 KVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMK-FVEASAQHKVDLYWIK 126 +V + TDS Y +QWI W++ GWKT+DKK VKN+DL + + + KV L W+ Sbjct: 67 EVNIVTDSQYALGIITQWIHNWKKRGWKTADKKPVKNVDLVNQIIEQLIKKEKVYLAWVP 126 Query: 127 GHAGNQENEKVDRIARNAA 145 H G NE+VD++ Sbjct: 127 AHKGIGGNEQVDKLVSAGI 145 >2zd1_A Reverse transcriptase/ribonuclease H; P51/P66, hetero dimer, NNRTI, nonnucleoside inhibitor, AIDS, HIV, rilpivirine, diarylpyrimidine, DAPY, DNA recombination; HET: T27; 1.80A {Human immunodeficiency virus 1} PDB: 2ze2_A* 3bgr_A* 1dlo_A 1bqm_A 2be2_A* 1s6q_A* 1s6p_A* 1s9g_A* 1suq_A* 2b5j_A* 2b6a_A* 2ban_A* 1s9e_A* 1hni_A* 1hnv_A* 1tvr_A* 2hmi_A* 2vg5_A* 2vg6_A* 2vg7_A* ... (A:430-557) Length = 128 Score = 65.8 bits (159), Expect = 2e-12 Identities = 30/136 (22%), Positives = 43/136 (31%), Gaps = 18/136 (13%) Query: 9 VHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCK 68 Y DGA + G G + + TTN + EL A AL + Sbjct: 11 ETFYVDGAANRETKLGKAGYVTNK---GRQKVVPLTNTTNQKTELQAIYLALQ--DSGLE 65 Query: 69 VLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128 V + TDS Y K + + + KV L W+ H Sbjct: 66 VNIVTDSQYALGIIQAQPDKSESELV-------------NQIIEQLIKKEKVYLAWVPAH 112 Query: 129 AGNQENEKVDRIARNA 144 G NE+VD++ Sbjct: 113 KGIGGNEQVDKLVSAG 128 >3c4h_A Poly(ADP-ribose) polymerase 3; enzyme-inhibitor complex, catalytic fragment, structural genomics, structural genomics consortium, SGC; HET: DRL; 2.10A {Homo sapiens} PDB: 3c49_A* 2pa9_A* 3ce0_A* 3fhb_A* (A:148-357) Length = 210 Score = 28.2 bits (62), Expect = 0.48 Identities = 11/66 (16%), Positives = 20/66 (30%), Gaps = 11/66 (16%) Query: 84 QWIKKWQQNGWKTSDKKTVKNI------DLWMKFVEASAQHKVDLYWIKGHAGNQENEKV 137 + I+ + + T+++I +F S L W H N V Sbjct: 15 KVIQTYLEQTGSNHRCPTLQHIWKVNQEGEEDRFQAHSKLGNRKLLW---HGTNMAV--V 69 Query: 138 DRIARN 143 I + Sbjct: 70 AAILTS 75 >2cvx_A Ribonucleoside-diphosphate reductase large chain 1; eukaryotic, ribonucleotide reductase, DNTP regulation, oxidoreductase; HET: DGT ADP; 2.20A {Saccharomyces cerevisiae} PDB: 1zyz_A 2cvs_A 2cvt_A* 2cvu_A* 2cvv_A* 1zzd_A* 2cvw_A* 2cvy_A* 2eud_A* 2zlf_A 2zlg_A* (A:167-616,A:689-888) Length = 650 Score = 27.1 bits (59), Expect = 1.1 Identities = 8/41 (19%), Positives = 14/41 (34%) Query: 74 DSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEA 114 + + + + K KT+K LW +EA Sbjct: 189 SAPGLSDCYGDEFEALYTRYEKEGRGKTIKAQKLWYSILEA 229 >1d5t_A Guanine nucleotide dissociation inhibitor; ultra-high resolution; 1.04A {Bos taurus} (A:108-122,A:289-395) Length = 122 Score = 25.9 bits (57), Expect = 2.4 Identities = 9/28 (32%), Positives = 14/28 (50%) Query: 33 KGKEKIISGGEKETTNNRMELMAAIKAL 60 +GK I+ ETT+ E+ A+ L Sbjct: 75 QGKYIAIASTTVETTDPEKEVEPALGLL 102 >2r9f_A Calpain-1 catalytic subunit; protease, peptidase, inhibitor, alpha-ketoamide, calcium, cytoplasm, hydrolase, membrane, thiol protease; HET: K2Z; 1.60A {Rattus norvegicus} (A:1-194) Length = 194 Score = 24.8 bits (53), Expect = 6.0 Identities = 9/42 (21%), Positives = 17/42 (40%) Query: 53 LMAAIKALTALKYPCKVLLYTDSSYVHKGFSQWIKKWQQNGW 94 L+AAI +LT + ++ S+ + + Q G Sbjct: 92 LLAAIASLTLNETILHRVVPYGQSFQEGYAGIFHFQLWQFGE 133 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.315 0.131 0.408 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,175,880 Number of extensions: 48056 Number of successful extensions: 178 Number of sequences better than 10.0: 1 Number of HSP's gapped: 161 Number of HSP's successfully gapped: 24 Length of query: 152 Length of database: 4,956,049 Length adjustment: 81 Effective length of query: 71 Effective length of database: 2,217,844 Effective search space: 157466924 Effective search space used: 157466924 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 (21.6 bits) S2: 51 (24.3 bits)