RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (268 letters) >3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.30A {Bordetella pertussis} (A:) Length = 173 Score = 98.4 bits (244), Expect = 8e-22 Identities = 50/168 (29%), Positives = 75/168 (44%), Gaps = 6/168 (3%) Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGW--PSEKARSSSANA 64 + I P N+G ARA+ +L LV PR +A + ++ A Sbjct: 3 AXTQAFSRVRFIXTQPSHPGNVGSAARAIKTXGFGELVLVAPRFPDXTAQPEAVALASGA 62 Query: 65 DCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKE---AAIVLNERIFSGQNV 121 V++ V L+EA+A + +A T R R+ +E A + +G V Sbjct: 63 LDVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAG-VV 121 Query: 122 GIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 I+ G ER GLTN +I L + I P NP + SLN++QA+ L WE Sbjct: 122 AIVLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWELR 169 >3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima} (X:) Length = 192 Score = 93.4 bits (231), Expect = 3e-20 Identities = 20/166 (12%), Positives = 50/166 (30%), Gaps = 12/166 (7%) Query: 14 GPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWP-----------SEKARSSSA 62 I+ ++ +AR +NL +V + Sbjct: 17 KDGSIISTAVTNLDVHDIARTARTYNLKGYYIVTNLRAQQDMVSKMLKFWREGFGSRYNP 76 Query: 63 NADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVG 122 + + V++ S L++ + D+ + + I + Sbjct: 77 SRAESLKLVKLKSYLEDVLEDIESVEGERPLIFFTSAKKRENDISFEEGRRIIIETEKPV 136 Query: 123 IIFGRERWGLTNEEIALSNAIISF-PVNPLFPSLNISQAVLLMVWE 167 +I WGL +E + +S+ ++ F L++ A +++ Sbjct: 137 LILLGTGWGLPDEILEISDYVLEPIRAQSDFNHLSVRAAAAIIIDR 182 >3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} (A:1-174) Length = 174 Score = 91.0 bits (225), Expect = 2e-19 Identities = 53/157 (33%), Positives = 88/157 (56%), Gaps = 5/157 (3%) Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72 + I+L++ NIG ARA LTQL LV+P+ E++ + SA A+ ++ + R Sbjct: 6 ENIRIVLIETSHSGNIGSAARAXKTXGLTQLCLVSPK--SVDEQSYALSAGAENIVKNAR 63 Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132 V + EA+ D + T+AR R+ +++ P+E A + + + I+FGRER GL Sbjct: 64 VVDSFDEAVDDCSLVIGTSARLRHLQNTLIEPRECAE---KVVAYKGKIAIVFGRERIGL 120 Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 TNEE+ + ++ P NP + SLN++ AV L+ +E Sbjct: 121 TNEELLKCHYHLNIPANPDYSSLNLAXAVQLVSYELR 157 >3ic6_A Putative methylase family protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; 2.59A {Neisseria gonorrhoeae fa 1090} (A:1-201) Length = 201 Score = 89.2 bits (220), Expect = 5e-19 Identities = 48/183 (26%), Positives = 79/183 (43%), Gaps = 19/183 (10%) Query: 6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWP------------ 53 P L + IIL NIG ARA L +L +V P Sbjct: 9 PALPDYLGNIRIILTRTSHPANIGSAARAXKTXGLHRLTIVTPNLXATPXTENPPVFNPD 68 Query: 54 -------SEKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKE 106 E++ ++ A V+ + + + L EA+AD A T+R R + P++ Sbjct: 69 DVQSFALPEESFILASGAADVLHNAEIVATLDEALADTTIACALTSRRREITAPLQTPRD 128 Query: 107 AAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVW 166 L + G+ V ++FG E +GL+ EE+ N + + NP + SLN++QAV ++ + Sbjct: 129 LVPELLQAANRGEKVALVFGNETFGLSIEEVRACNRLXTINGNPDYFSLNLAQAVQVVCY 188 Query: 167 ECM 169 E Sbjct: 189 EIF 191 >1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* (A:119-287) Length = 169 Score = 86.9 bits (214), Expect = 3e-18 Identities = 26/163 (15%), Positives = 50/163 (30%), Gaps = 6/163 (3%) Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADC 66 ++ ++ P NIG + R+ L + K+ SS + Sbjct: 1 RIPVREDFLGVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPKSVRSSTGSLF 60 Query: 67 VIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFG 126 + + E + R ++ E Q ++ G Sbjct: 61 SLP-AVRVPSPGEVXDWVE-----ARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIG 114 Query: 127 RERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 E GL+N L + +S P SLN + A +++E + Sbjct: 115 NETAGLSNAWRTLCDYTVSIPXAGSASSLNAANAATAILYEAV 157 >2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, knot, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.85A {Porphyromonas gingivalis W83} (A:99-257) Length = 159 Score = 86.5 bits (213), Expect = 3e-18 Identities = 25/169 (14%), Positives = 51/169 (30%), Gaps = 18/169 (10%) Query: 6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANAD 65 P ++ ++L Q N+G + R F + + L S K +S A Sbjct: 1 PVVEG----LTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQASXGAL 56 Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125 + + R + ++ + ++ Sbjct: 57 ARVQPTPL---------KNTVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEPAILVL 107 Query: 126 GRERWGLTNEEIALSNAIISFPVNPLFP-----SLNISQAVLLMVWECM 169 G E G++ E A ++ P + L SLN++ A ++ E Sbjct: 108 GSEGRGISPEVAAEITDRLTIPASGLSVKGHTESLNVAIATAILCSEWR 156 >1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} (A:21-176) Length = 156 Score = 83.8 bits (206), Expect = 2e-17 Identities = 28/154 (18%), Positives = 59/154 (38%), Gaps = 12/154 (7%) Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75 ++L + N+ + R + + VNP G P+ S ++ + Sbjct: 4 TVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVPTFNETSGGSHKWVYLRVHPDLH 63 Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135 + + F TA + + + ++FG E+WG++ E Sbjct: 64 EAFRFLKERGFTVYATALREDARDF------------REVDYTKPTAVLFGAEKWGVSEE 111 Query: 136 EIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 +AL++ I P+ + SLN+S A ++++E Sbjct: 112 ALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQ 145 >1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli} (A:90-253) Length = 164 Score = 83.3 bits (205), Expect = 3e-17 Identities = 24/162 (14%), Positives = 55/162 (33%), Gaps = 11/162 (6%) Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67 + + + ++IL N+G R+ + + + R + A+ + A Sbjct: 10 IASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAES 69 Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127 + +RV + + T + ++ A + + ++ G Sbjct: 70 VPLIRVTN-----------LARTXRXLQEENIWIVGTAGEADHTLYQSKXTGRLALVXGA 118 Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 E G + +IS P SLN+S A + ++E + Sbjct: 119 EGEGXRRLTREHCDELISIPXAGSVSSLNVSVATGICLFEAV 160 >3gyq_A RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltransferase, spout mtases, SAM, trefoil knot, antibiotic resistance; HET: SAM; 2.45A {Streptomyces cyaneus} (A:113-272) Length = 160 Score = 83.0 bits (204), Expect = 4e-17 Identities = 26/155 (16%), Positives = 61/155 (39%), Gaps = 10/155 (6%) Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72 +G V++L ++ NIG + R + + LV+ +++ ++ V Sbjct: 6 RGDVVVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIADRRLQRASRGYVFSLPVV 65 Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132 + A + + + + I + E + + ++FG E+ G Sbjct: 66 LSGRE----------EAIAFIRDSGMQLMTLKADGDISVKELGDNPDRLALLFGSEKGGP 115 Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167 ++ S+A +S P+ SLN+S ++ + + E Sbjct: 116 SDLFEEASSASVSIPMMSQTESLNVSVSLGIALHE 150 >1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} (A:24-180) Length = 157 Score = 82.6 bits (203), Expect = 4e-17 Identities = 18/157 (11%), Positives = 56/157 (35%), Gaps = 11/157 (7%) Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72 K ++ + + N + R + L + ++ + + + + Sbjct: 1 KDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHAEG-KKAKINEGITQGSHKWVFIEK 59 Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132 V + +++ + + + A + + + ++ G E G+ Sbjct: 60 VDNPVQKLLEFKNRGFQIVATWLSKESVNFREVDY----------TKPTVLVVGNELQGV 109 Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 + E + +++ I P+ + SLN+S A ++++E Sbjct: 110 SPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQ 146 >1ipa_A RRMH, RNA 2'-O-ribose methyltransferase; DEEP trefoil knot, rossmann fold, EL30-like fold, riken structural genomics/proteomics initiative; 2.40A {Thermus thermophilus} (A:109-274) Length = 166 Score = 78.7 bits (193), Expect = 7e-16 Identities = 26/164 (15%), Positives = 54/164 (32%), Gaps = 15/164 (9%) Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADC 66 + + S +++ V + N+G V R+ + + D + + R+S+ Sbjct: 1 EYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVFS 60 Query: 67 V-IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125 + + L + ATT + AI Sbjct: 61 LRTLAASESEVLDWIKQHNLPLVATTPHAEALYWEANLRPPVAI--------------AV 106 Query: 126 GRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 G E GL + + + P+ SLN+S + L+++E + Sbjct: 107 GPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEAL 150 >2ha8_A TAR (HIV-1) RNA loop binding protein; methyltransferase, structural genomics, structural genomics consortium, SGC, RNA binding protein; HET: SAH; 1.60A {Homo sapiens} (A:) Length = 184 Score = 78.4 bits (192), Expect = 9e-16 Identities = 24/162 (14%), Positives = 56/162 (34%), Gaps = 9/162 (5%) Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67 L S +++ N+G + R F + L + + + ++ + S +A+ Sbjct: 20 LGKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQC-ISDKQFQHLSVSAEQW 78 Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127 + V V + + + + A + + + ++ G Sbjct: 79 LPLVEVKPPQLI--------DYLQQKKTEGYTIIGVEQTAKSLDLTQYCFPEKSLLLLGN 130 Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 ER G+ I + + P + SLN+ + L++WE Sbjct: 131 EREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYT 172 >1mxi_A YIBK, hypothetical tRNA/RRNA methyltransferase HI0766; S-adenosylhomocysteine, SPOU family, structure 2 function project; HET: SAH; 1.70A {Haemophilus influenzae} (A:) Length = 160 Score = 76.8 bits (188), Expect = 3e-15 Identities = 22/156 (14%), Positives = 47/156 (30%), Gaps = 15/156 (9%) Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75 I+L +P++ +N G + R N + W ++ R S + + R Sbjct: 3 DIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRH-K 61 Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135 + + + + ++FG E G+ Sbjct: 62 TFEAFLESEKPKRLFALTTKGCPAHSQVKFK------------LGDYLMFGPETRGIPMS 109 Query: 136 EIALSNAIISF--PVNPLFPSLNISQAVLLMVWECM 169 + P+ S+N+S +V + V+E Sbjct: 110 ILNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAW 145 >3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} (A:) Length = 160 Score = 74.1 bits (181), Expect = 2e-14 Identities = 27/156 (17%), Positives = 44/156 (28%), Gaps = 13/156 (8%) Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75 ++LV+P++ N G V R N + K R + + Sbjct: 7 NVVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRD 66 Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135 A A + + A +FG E GL Sbjct: 67 W-----------DAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPA 115 Query: 136 EIALSNAIISF--PVNPLFPSLNISQAVLLMVWECM 169 + P+ P SLN+S V ++V+E Sbjct: 116 LVDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAW 151 >3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} (A:175-244) Length = 70 Score = 61.9 bits (151), Expect = 9e-11 Identities = 16/72 (22%), Positives = 32/72 (44%), Gaps = 4/72 (5%) Query: 186 PATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVST 245 T +L F DY E + G+ + + + L ++ R +L + E+ +L G +S Sbjct: 3 YPTTDQLAYFFDYTERIYQSLGFIQN----QGVXRKLKRLYYRAKLEKNELNILNGXLSA 58 Query: 246 LDKFSRQSSRRN 257 ++K + N Sbjct: 59 VEKRIDLTKEDN 70 >2k3i_A Uncharacterized protein YIIS; GFT protein structure, PSI, NESG, structural genomics, protein structure initiative; NMR {Shigella flexneri 2A} (A:) Length = 109 Score = 27.1 bits (60), Expect = 2.8 Identities = 15/70 (21%), Positives = 24/70 (34%), Gaps = 8/70 (11%) Query: 63 NADCVIDSVRVFSNLKEAIADLHFIYATTARNR------NNFKSVLAPKEAAIVLNERI- 115 N +C R F+ +EA + + A + + E + L+ Sbjct: 25 NDNCTSKFSRFFATREEAESFMTK-LKELAAAASSADEGASVAYKIKDLEGQVELDAAFT 83 Query: 116 FSGQNVGIIF 125 FS Q IIF Sbjct: 84 FSCQAEMIIF 93 >2w3s_B Xanthine dehydrogenase; XO, XDH, GOUT, iron, 2Fe-2S, iron-sulfur, oxidoreductase, purine metabolism, molybdenum cofactor, hypoxanthine; HET: MPN FAD XAN; 2.60A {Rhodobacter capsulatus} PDB: 1jrp_B* 2w3r_B* 1jro_B* 2w54_B* 2w55_B* (B:462-606) Length = 145 Score = 26.0 bits (57), Expect = 4.8 Identities = 7/46 (15%), Positives = 15/46 (32%) Query: 166 WECMENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRP 211 C ++ V+ E+++ ISL G++ Sbjct: 98 EGCAARDVIFDAGQVQASGKSWRFAEIVAAAYMARISLSATGFYAT 143 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 0.318 0.133 0.380 Gapped Lambda K H 0.267 0.0477 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,896,878 Number of extensions: 83144 Number of successful extensions: 204 Number of sequences better than 10.0: 1 Number of HSP's gapped: 188 Number of HSP's successfully gapped: 18 Length of query: 268 Length of database: 4,956,049 Length adjustment: 87 Effective length of query: 181 Effective length of database: 2,015,014 Effective search space: 364717534 Effective search space used: 364717534 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 (21.7 bits) S2: 54 (25.2 bits)