RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780516|ref|YP_003064929.1| type II modification methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (83 letters) >1g55_A DNA cytosine methyltransferase DNMT2; human DNA methyltransferase homologue; HET: DNA SAH; 1.80A {Homo sapiens} SCOP: c.66.1.26 Length = 343 Score = 91.6 bits (226), Expect = 3e-20 Identities = 23/85 (27%), Positives = 46/85 (54%), Gaps = 5/85 (5%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNT-LIFGDIAKIK 60 L++ +L+ G+GG+ L ++ + + ++N + + Y+ NFP+T L+ I I Sbjct: 3 LRVLELYSGVGGMHHALRESC--IPAQVVAAIDVNTVANEVYKYNFPHTQLLAKTIEGIT 60 Query: 61 TQDIP--DHDVLLAGFPCQPFSQAG 83 ++ D++L PCQPF++ G Sbjct: 61 LEEFDRLSFDMILMSPPCQPFTRIG 85 >3me5_A Cytosine-specific methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium; 1.75A {Shigella flexneri 2A} PDB: 3lx6_A Length = 482 Score = 86.8 bits (214), Expect = 1e-18 Identities = 41/101 (40%), Positives = 49/101 (48%), Gaps = 24/101 (23%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPN----TLIFGDIAK 58 + DLF GIGGIR E +C F+SE N ++V+TY+AN DI Sbjct: 90 RFIDLFAGIGGIRRGFESI----GGQCVFTSEWNKHAVRTYKANHYCDPATHHFNEDIRD 145 Query: 59 IKTQD----------------IPDHDVLLAGFPCQPFSQAG 83 I IP+HDVLLAGFPCQPFS AG Sbjct: 146 ITLSHQEGVSDEAAAEHIRQHIPEHDVLLAGFPCQPFSLAG 186 >1dct_A Protein (modification methylase HAEIII); enzyme, cytosine methylase; HET: DNA C49 5CM; 2.80A {Haemophilus aegyptus} SCOP: c.66.1.26 Length = 324 Score = 80.8 bits (198), Expect = 6e-17 Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 4/79 (5%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61 + + LF G GG+ L ++ ++E + KTY++N LI GDI+KI + Sbjct: 1 MNLISLFSGAGGLDLGFQKA----GFRIICANEYDKSIWKTYESNHSAKLIKGDISKISS 56 Query: 62 QDIPDHDVLLAGFPCQPFS 80 + P D ++ G PCQ +S Sbjct: 57 DEFPKCDGIIGGPPCQSWS 75 >2c7p_A Modification methylase HHAI; DNA methyltransferase, methyltransferase, base flipping, restriction system, transferase; HET: 5CM A1P SAH EPE CIT; 1.7A {Haemophilus haemolyticus} SCOP: c.66.1.26 PDB: 10mh_A* 1m0e_A* 1mht_A* 1hmy_A* 1skm_A* 2c7o_A* 2c7q_A* 2hmy_B* 2hr1_A* 3mht_A* 4mht_A* 5mht_A* 6mht_A* 7mht_A* 8mht_A* 9mht_A* 2zcj_A* 2z6u_A* 2z6q_A* 2uz4_A* ... Length = 327 Score = 79.3 bits (194), Expect = 2e-16 Identities = 37/82 (45%), Positives = 50/82 (60%), Gaps = 5/82 (6%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61 L+ DLF G+GG RL LE EC +S+E + Y+ + Y+ NF GDI ++ Sbjct: 12 LRFIDLFAGLGGFRLALESC----GAECVYSNEWDKYAQEVYEMNFGEK-PEGDITQVNE 66 Query: 62 QDIPDHDVLLAGFPCQPFSQAG 83 + IPDHD+L AGFPCQ FS +G Sbjct: 67 KTIPDHDILCAGFPCQAFSISG 88 >3g7u_A Cytosine-specific methyltransferase; DNA-binding, NAD-binding, structural genomics, protein structure initiative, PSI; 1.75A {Escherichia coli O157} Length = 376 Score = 71.3 bits (173), Expect = 5e-14 Identities = 24/89 (26%), Positives = 43/89 (48%), Gaps = 12/89 (13%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTL-IFGDIAKIK 60 L + DLF G+GG+ L + + + EI+ +++ T+ NFP +L + D++ + Sbjct: 3 LNVIDLFSGVGGLSLGAARA----GFDVKMAVEIDQHAINTHAINFPRSLHVQEDVSLLN 58 Query: 61 TQDIPDH-------DVLLAGFPCQPFSQA 82 + I D ++ G PCQ FS Sbjct: 59 AEIIKGFFKNDMPIDGIIGGPPCQGFSSI 87 >2qrv_A DNA (cytosine-5)-methyltransferase 3A; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens} Length = 295 Score = 66.9 bits (162), Expect = 1e-12 Identities = 18/83 (21%), Positives = 36/83 (43%), Gaps = 6/83 (7%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIF-GDIAKIK 60 +++ LF GI L L+ V+ + +SE+ S+ +++ GD+ + Sbjct: 17 IRVLSLFDGIATGLLVLKDL--GIQVDRYIASEVCEDSITVGMVRHQGKIMYVGDVRSVT 74 Query: 61 ---TQDIPDHDVLLAGFPCQPFS 80 Q+ D+++ G PC S Sbjct: 75 QKHIQEWGPFDLVIGGSPCNDLS 97 >2qrv_B DNA (cytosine-5)-methyltransferase 3-like; DNA methyltransferase 3A (DNMT3A) and ITS regulatory factor; HET: DNA SAH; 2.89A {Homo sapiens} Length = 230 Score = 45.3 bits (107), Expect = 3e-06 Identities = 12/82 (14%), Positives = 24/82 (29%), Gaps = 23/82 (28%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61 +++ LF I L F S +P +K D+ Sbjct: 34 VRVLSLFEDIKKELTSLG----------FLESGSDPGQLKHV----------VDVTDTVR 73 Query: 62 QDIPDH---DVLLAGFPCQPFS 80 +D+ + D++ P + Sbjct: 74 KDVEEWGPFDLVYGATPPLGHT 95 >2pv0_B DNA (cytosine-5)-methyltransferase 3-like; DNMT3L, unmethylated H3K4, de novo DNA methylation, transferase regulator; HET: DNA; 3.30A {Homo sapiens} PDB: 2pvc_B* Length = 386 Score = 42.6 bits (100), Expect = 2e-05 Identities = 12/82 (14%), Positives = 23/82 (28%), Gaps = 23/82 (28%) Query: 2 LKITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKT 61 +++ LF I L F S +P +K D+ Sbjct: 190 VRVLSLFEDIKKELTSLG----------FLESGSDPGQLKH----------VVDVTDTVR 229 Query: 62 QDI---PDHDVLLAGFPCQPFS 80 +D+ D++ P + Sbjct: 230 KDVEEWGPFDLVYGATPPLGHT 251 >2ozv_A Hypothetical protein ATU0636; structural genomics, predicted transferase, predicted O-methyltransferase, PFAM PF05175, PSI-2; HET: MSE; 1.70A {Agrobacterium tumefaciens str} Length = 260 Score = 30.9 bits (69), Expect = 0.066 Identities = 10/81 (12%), Positives = 21/81 (25%), Gaps = 5/81 (6%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIK-- 60 +I DL G G + + V + E + + + + A+I+ Sbjct: 39 RIADLGAGAGAAGMAVAARLEKAEVTLY---ERSQEMAEFARRSLELPDNAAFSARIEVL 95 Query: 61 TQDIPDHDVLLAGFPCQPFSQ 81 D+ Sbjct: 96 EADVTLRAKARVEAGLPDEHF 116 >3ll7_A Putative methyltransferase; methytransferase, structural genomics, MCSG, PSI-2, protein structure initiative; HET: MSE; 1.80A {Porphyromonas gingivalis} Length = 410 Score = 28.8 bits (64), Expect = 0.33 Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 5/65 (7%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKTQ 62 K+ DL G+G + L E N + + N P L G I T Sbjct: 96 KVVDLTGGLGIDFIAL-----MSKASQGIYIERNDETAVAARHNIPLLLNEGKDVNILTG 150 Query: 63 DIPDH 67 D ++ Sbjct: 151 DFKEY 155 >2ih2_A Modification methylase TAQI; DNA, DNA methyltransferase, target base partner, 5- methylpyrimidin-2(1H)-ONE, base flipping; HET: 5PY 6MA NEA; 1.61A {Thermus aquaticus} SCOP: c.66.1.27 d.287.1.1 PDB: 2ibs_A* 2ibt_A* 2ih4_A* 2ih5_A* 2jg3_A* 2np6_A* 2np7_A* 1aqj_A* 1aqi_A* 2adm_A* 1g38_A* Length = 421 Score = 26.4 bits (57), Expect = 1.4 Identities = 10/72 (13%), Positives = 21/72 (29%), Gaps = 5/72 (6%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKTQ 62 ++ + C G + H F EI+P ++ I D + Sbjct: 42 RVLEPACAHGPFLRAFRE--AHGTAYRFVGVEIDPKALDLPPW---AEGILADFLLWEPG 96 Query: 63 DIPDHDVLLAGF 74 + D + + Sbjct: 97 EAFDLILGNPPY 108 >3gdh_A Trimethylguanosine synthase homolog; M7G, CAP, dimethyltransferase, usnRNA, snoRNA, telomerase, cytoplasm, methyltransferase, nucleus; HET: MGP SAH; 2.00A {Homo sapiens} PDB: 3egi_A* Length = 241 Score = 25.9 bits (56), Expect = 2.3 Identities = 15/82 (18%), Positives = 24/82 (29%), Gaps = 8/82 (9%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSE----INPYSVKTYQANFPNTLIFGDIAK 58 + D FCG+GG + T V + + + Y I GD Sbjct: 81 VVVDAFCGVGGNTIQFALTGMR--VIAIDIDPVKIALARNNAEVYGIADKIEFICGDFLL 138 Query: 59 IKTQDIPDHDVLLAGFPCQPFS 80 + + DV+ P Sbjct: 139 LASFL--KADVVFLSPPWGGPD 158 >2as0_A Hypothetical protein PH1915; RNA methyltransferase, structural genomics, PSI, protein structure initiative; 1.80A {Pyrococcus horikoshii} SCOP: b.122.1.9 c.66.1.51 Length = 396 Score = 25.9 bits (56), Expect = 2.5 Identities = 7/45 (15%), Positives = 18/45 (40%), Gaps = 4/45 (8%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANF 47 ++ D+F GG + + + +P +++T + N Sbjct: 220 RVLDVFTYTGGFAIHA----AIAGADEVIGIDKSPRAIETAKENA 260 >1ne2_A Hypothetical protein TA1320; structural genomics, conserved hypothetical protein, PSI, protein structure initiative; 1.75A {Thermoplasma acidophilum} SCOP: c.66.1.32 Length = 200 Score = 25.0 bits (54), Expect = 4.5 Identities = 9/47 (19%), Positives = 18/47 (38%), Gaps = 4/47 (8%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPN 49 + D G G + +V F +I+P +++T + N Sbjct: 54 SVIDAGTGNGILACGSYL-LGAESVTAF---DIDPDAIETAKRNCGG 96 >3a27_A TYW2, uncharacterized protein MJ1557; wybutosine modification, transferase; HET: SAM; 2.00A {Methanocaldococcus jannaschii} Length = 272 Score = 24.7 bits (53), Expect = 5.4 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 3/39 (7%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVK 41 + D+F GIG + L + + V E NP + Sbjct: 122 VVVDMFAGIGYFTIPLAKYSKPKLVYAI---EKNPTAYH 157 >1l3i_A Precorrin-6Y methyltransferase/putative decarboxylase; structural genomics, beta barrel, rossmann fold, tetramer; HET: SAH; 1.95A {Methanothermobacterthermautotrophicus} SCOP: c.66.1.22 PDB: 1kxz_A 1l3b_A 1f38_A 1l3c_A* Length = 192 Score = 24.3 bits (52), Expect = 6.8 Identities = 16/78 (20%), Positives = 30/78 (38%), Gaps = 12/78 (15%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPN-------TLIFGD 55 D+ CG GG+ L+L ++ + NP ++ T + N TL+ GD Sbjct: 36 VAVDVGCGTGGVTLELAGRVRR-----VYAIDRNPEAISTTEMNLQRHGLGDNVTLMEGD 90 Query: 56 IAKIKTQDIPDHDVLLAG 73 + + ++ G Sbjct: 91 APEALCKIPDIDIAVVGG 108 >3lpm_A Putative methyltransferase; structural genomics, protein structure initiative, NEW YORK structural genomix research consortium, nysgxrc; 2.40A {Listeria monocytogenes} Length = 259 Score = 24.2 bits (52), Expect = 7.4 Identities = 11/45 (24%), Positives = 14/45 (31%), Gaps = 4/45 (8%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANF 47 KI DL G G I L L + EI + + Sbjct: 52 KIIDLCSGNGIIPLLLSTRTKAK----IVGVEIQERLADMAKRSV 92 >2yx1_A Hypothetical protein MJ0883; methyl transferase, tRNA modification enzyme; HET: SFG; 2.20A {Methanocaldococcus jannaschii} Length = 336 Score = 24.0 bits (51), Expect = 8.1 Identities = 8/39 (20%), Positives = 21/39 (53%), Gaps = 6/39 (15%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVK 41 + D+F G+G + +N + ++ +INP++++ Sbjct: 198 VVVDMFAGVGPFSIA------CKNAKKIYAIDINPHAIE 230 >3jwg_A HEN1, methyltransferase type 12; 1.90A {Clostridium thermocellum} PDB: 3jwi_A Length = 219 Score = 23.8 bits (50), Expect = 8.9 Identities = 8/32 (25%), Positives = 13/32 (40%) Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSE 34 K+ DL CG G + L + + + S Sbjct: 32 KVIDLGCGEGNLLSLLLKDKSFEQITGVDVSY 63 >1eh9_A Glycosyltrehalose trehalohydrolase; alpha/beta barrel, calcium binding, covalent dimer,; 3.00A {Sulfolobus solfataricus} SCOP: b.1.18.2 b.71.1.1 c.1.8.1 PDB: 1eha_A Length = 558 Score = 23.6 bits (50), Expect = 9.6 Identities = 11/43 (25%), Positives = 21/43 (48%) Query: 13 GIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGD 55 G+ + L+ +NH E + ++ PY + Y+ + T F D Sbjct: 181 GLGVILDVVYNHVGPEGNYMVKLGPYFSQKYKTPWGLTFNFDD 223 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.325 0.143 0.447 Gapped Lambda K H 0.267 0.0476 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 710,942 Number of extensions: 25506 Number of successful extensions: 96 Number of sequences better than 10.0: 1 Number of HSP's gapped: 86 Number of HSP's successfully gapped: 23 Length of query: 83 Length of database: 5,693,230 Length adjustment: 51 Effective length of query: 32 Effective length of database: 4,456,786 Effective search space: 142617152 Effective search space used: 142617152 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 50 (23.7 bits)