RPS-BLAST 2.2.22 [Sep-27-2009] Database: scop70_1_75 13,730 sequences; 2,407,596 total letters Searching..................................................done Query= gi|254780796|ref|YP_003065209.1| ribonuclease H [Candidatus Liberibacter asiaticus str. psy62] (152 letters) >d1rila_ c.55.3.1 (A:) RNase H (RNase HI) {Thermus thermophilus [TaxId: 274]} Length = 147 Score = 123 bits (308), Expect = 9e-30 Identities = 76/140 (54%), Positives = 98/140 (70%), Gaps = 1/140 (0%) Query: 7 REVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYP 66 + V +TDGAC GNPGPGGW LLR+ EK++SGGE TTNNRMEL AAI+ L ALK P Sbjct: 2 KRVALFTDGACLGNPGPGGWAALLRFHAHEKLLSGGEACTTNNRMELKAAIEGLKALKEP 61 Query: 67 CKVLLYTDSSYVHKGFSQWIKKWQQ-NGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWI 125 C+V LYTDS Y+ K F++ + + GW+T++ K VKN DLW + A A H+V +++ Sbjct: 62 CEVDLYTDSHYLKKAFTEGWLEGWRKRGWRTAEGKPVKNRDLWEALLLAMAPHRVRFHFV 121 Query: 126 KGHAGNQENEKVDRIARNAA 145 KGH G+ ENE+VDR AR A Sbjct: 122 KGHTGHPENERVDREARRQA 141 >d1zbfa1 c.55.3.1 (A:62-193) BH0863-like Ribonuclease H {Bacillus halodurans [TaxId: 86665]} Length = 132 Score = 121 bits (304), Expect = 3e-29 Identities = 27/131 (20%), Positives = 44/131 (33%), Gaps = 11/131 (8%) Query: 12 YTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYP-CKVL 70 D GNPG + + G+ TNN E +A + L LK + Sbjct: 8 SVDVGSQGNPGIVEYKGVDTKTGEVLFEREPIPIGTNNMGEFLAIVHGLRYLKERNSRKP 67 Query: 71 LYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASA---QHKVDLYWIKG 127 +Y++S K W+K K++ + + +W EA H + +K Sbjct: 68 IYSNSQTAIK----WVKDK---KAKSTLVRNEETALIWKLVDEAEEWLNTHTYETPILKW 120 Query: 128 HAGNQENEKVD 138 K D Sbjct: 121 QTDKWGEIKAD 131 >d1jl1a_ c.55.3.1 (A:) RNase H (RNase HI) {Escherichia coli [TaxId: 562]} Length = 152 Score = 120 bits (301), Expect = 6e-29 Identities = 78/139 (56%), Positives = 101/139 (72%) Query: 7 REVHAYTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYP 66 ++V +T G+ GNPGPGG+G +LRY+G+EK S G TTNNRMELMAAI AL ALK Sbjct: 1 KQVEIFTAGSALGNPGPGGYGAILRYRGREKTFSAGYTRTTNNRMELMAAIVALEALKEH 60 Query: 67 CKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIK 126 +V+L TDS YV +G +QWI W++ GWKT+DKK VKN+DLW + A QH++ W+K Sbjct: 61 AEVILSTDSQYVRQGITQWIHNWKKRGWKTADKKPVKNVDLWQRLDAALGQHQIKWEWVK 120 Query: 127 GHAGNQENEKVDRIARNAA 145 GHAG+ ENE+ D +AR AA Sbjct: 121 GHAGHPENERADELARAAA 139 >d1s1ta1 c.55.3.1 (A:430-539) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 1 [TaxId: 11676]} Length = 110 Score = 95.4 bits (237), Expect = 2e-21 Identities = 25/117 (21%), Positives = 38/117 (32%), Gaps = 18/117 (15%) Query: 12 YTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCKVLL 71 Y DGA + G G + + +TTN + EL A AL +V + Sbjct: 12 YVDGAANRETKLGKAGYVTNR---GRQKVVTLTDTTNQKTELQAIYLALQDS--GLEVNI 66 Query: 72 YTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGH 128 TDS Y + + ++ +K KV L W+ H Sbjct: 67 VTDSQYALGIIQAQPDQSESELVNQIIEQLIKK-------------EKVYLAWVPAH 110 >d1mu2a1 c.55.3.1 (A:430-555) HIV RNase H (Domain of reverse transcriptase) {Human immunodeficiency virus type 2 [TaxId: 11709]} Length = 126 Score = 90.0 bits (222), Expect = 8e-20 Identities = 27/133 (20%), Positives = 44/133 (33%), Gaps = 18/133 (13%) Query: 12 YTDGACSGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAIKALTALKYPCKVLL 71 YTDG+C+ G G + K ++TTN + EL A KV + Sbjct: 11 YTDGSCNRQSKEGKAGY---VTDRGKDKVKKLEQTTNQQAELEAFAM--ALTDSGPKVNI 65 Query: 72 YTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIKGHAGN 131 DS YV + + + E + + + W+ H G Sbjct: 66 IVDSQYVMGIVASQPTESESKIV-------------NQIIEEMIKKEAIYVAWVPAHKGI 112 Query: 132 QENEKVDRIARNA 144 N++VD + Sbjct: 113 GGNQEVDHLVSQG 125 >d1d5ta2 d.16.1.6 (A:292-388) Guanine nucleotide dissociation inhibitor, GDI {Cow (Bos taurus) [TaxId: 9913]} Length = 97 Score = 26.2 bits (58), Expect = 1.3 Identities = 9/28 (32%), Positives = 14/28 (50%) Query: 33 KGKEKIISGGEKETTNNRMELMAAIKAL 60 +GK I+ ETT+ E+ A+ L Sbjct: 55 QGKYIAIASTTVETTDPEKEVEPALGLL 82 >d1rf6a_ d.68.2.2 (A:) 5-enol-pyruvyl shikimate-3-phosphate (EPSP) synthase {Streptococcus pneumoniae [TaxId: 1313]} Length = 427 Score = 26.0 bits (56), Expect = 1.4 Identities = 11/63 (17%), Positives = 24/63 (38%), Gaps = 5/63 (7%) Query: 30 LRYKGKEKIISGGEKETTNN-RMELMAAIKALTALKYPCKVLLYTDSSYVHKGFSQWIKK 88 + KGK + G T + R+ +M AI AL ++ + ++ + + Sbjct: 365 MIIKGKSAL-HGARVNTFGDHRIGMMTAIAALLVADGEVEL---DRAEAINTSYPSFFDD 420 Query: 89 WQQ 91 + Sbjct: 421 LES 423 >d2bcgg3 d.16.1.6 (G:302-399) Guanine nucleotide dissociation inhibitor, GDI {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]} Length = 98 Score = 25.4 bits (56), Expect = 2.0 Identities = 10/28 (35%), Positives = 11/28 (39%) Query: 33 KGKEKIISGGEKETTNNRMELMAAIKAL 60 KG I ET +EL A K L Sbjct: 56 KGHYLAIISTIIETDKPHIELEPAFKLL 83 >d1q7ha2 d.17.6.2 (A:3-68) Hypothetical protein Ta1423, N-terminal domain {Archaeon Thermoplasma acidophilum [TaxId: 2303]} Length = 66 Score = 23.9 bits (51), Expect = 6.2 Identities = 8/23 (34%), Positives = 13/23 (56%) Query: 105 IDLWMKFVEASAQHKVDLYWIKG 127 ID+ + +E +AQ Y+I G Sbjct: 22 IDITGESLEVAAQKSASAYYIGG 44 >d1rwta_ f.43.1.1 (A:) Chlorophyll a-b binding protein {Spinach (Spinacia oleracea) [TaxId: 3562]} Length = 218 Score = 23.9 bits (51), Expect = 7.1 Identities = 7/40 (17%), Positives = 11/40 (27%) Query: 18 SGNPGPGGWGVLLRYKGKEKIISGGEKETTNNRMELMAAI 57 G + L E KE N R+ + + Sbjct: 140 DPLYPGGSFDPLGLADDPEAFAELKVKEIKNGRLAMFSMF 179 >d1ypzf1 b.1.1.1 (F:1-120) T-cell antigen receptor {Human (Homo sapiens), gamma-chain [TaxId: 9606]} Length = 120 Score = 23.2 bits (49), Expect = 9.4 Identities = 13/77 (16%), Positives = 27/77 (35%) Query: 67 CKVLLYTDSSYVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLYWIK 126 CKV + + S + Q + + T +D K +EAS + Sbjct: 23 CKVFIESFRSVTIHWYRQKPNQGLEFLLYVLATPTHIFLDKEYKKMEASKNPSASTSILT 82 Query: 127 GHAGNQENEKVDRIARN 143 ++ +E+E + + Sbjct: 83 IYSLEEEDEAIYYCSYG 99 >d2b5dx2 c.6.2.4 (X:1-404) Alpha-amylase AmyC {Thermotoga maritima [TaxId: 2336]} Length = 404 Score = 23.5 bits (50), Expect = 9.4 Identities = 7/47 (14%), Positives = 19/47 (40%), Gaps = 1/47 (2%) Query: 77 YVHKGFSQWIKKWQQNGWKTSDKKTVKNIDLWMKFVEASAQHKVDLY 123 + + + + ++K + K ++T K L K + +H + Sbjct: 69 DLQEKYERHMEKLIELANK-EVERTKKEHPLKHKMAKFYREHFEKIL 114 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 0.315 0.131 0.408 Gapped Lambda K H 0.267 0.0603 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 13730 Number of Hits to DB: 583,301 Number of extensions: 25332 Number of successful extensions: 93 Number of sequences better than 10.0: 1 Number of HSP's gapped: 84 Number of HSP's successfully gapped: 19 Length of query: 152 Length of database: 2,407,596 Length adjustment: 78 Effective length of query: 74 Effective length of database: 1,336,656 Effective search space: 98912544 Effective search space used: 98912544 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: 49 (22.9 bits)