RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780904|ref|YP_003065317.1| tRNA/rRNA methyltransferase [Candidatus Liberibacter asiaticus str. psy62] (268 letters) >3onp_A TRNA/RRNA methyltransferase (SPOU); structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG; 1.90A {Rhodobacter sphaeroides} Length = 249 Score = 182 bits (463), Expect = 7e-47 Identities = 97/239 (40%), Positives = 142/239 (59%), Gaps = 1/239 (0%) Query: 15 PVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVF 74 PV ILV PQ+GENIG ARAM NF L +LR+V+PRDGWP+ KA + ++ A ++D +F Sbjct: 5 PVFILVRPQMGENIGAAARAMLNFGLGRLRIVDPRDGWPNPKAVAMASGAGRLLDHAGLF 64 Query: 75 SNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTN 134 + EAI D +++ATTAR R K V+ P+ A G+ VGI+FG ER GL N Sbjct: 65 PTVAEAIRDCDYVFATTARGRELTKPVMTPERAMAHGRALTGEGRRVGILFGPERTGLEN 124 Query: 135 EEIALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKE-QNTPATKGELL 193 E++AL+NAI++ PVNP F SLN++Q VLL+ +E + + + + A+ E+ Sbjct: 125 EDVALANAIVTVPVNPEFFSLNLAQCVLLLAYEWRRQHDETPPEVIDMARVDFASGLEVE 184 Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQ 252 D+ E LE G+F P EK M +L +++ R L R +V L G++ + +Q Sbjct: 185 KLGDHFEEKLEAAGFFFPPEKAPGMKLNLRNMWARLPLTRADVQTLHGMLRQIAWKLKQ 243 >3ic6_A Putative methylase family protein; structural genomics, PSI-2, protein structure initiative, midwest center for structural genomics; 2.59A {Neisseria gonorrhoeae fa 1090} Length = 223 Score = 126 bits (317), Expect = 5e-30 Identities = 56/219 (25%), Positives = 99/219 (45%), Gaps = 20/219 (9%) Query: 1 MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPS------ 54 MT P L + IIL NIG ARAM L +L +V P Sbjct: 4 MTALKPALPDYLGNIRIILTRTSHPANIGSAARAMKTMGLHRLTIVTPNLMATPMTENPP 63 Query: 55 -------------EKARSSSANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSV 101 E++ ++ A V+ + + + L EA+AD A T+R R + Sbjct: 64 VFNPDDVQSFALPEESFILASGAADVLHNAEIVATLDEALADTTIACALTSRRREITAPL 123 Query: 102 LAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAV 161 P++ L + G+ V ++FG E +GL+ EE+ N +++ NP + SLN++QAV Sbjct: 124 QTPRDLVPELLQAANRGEKVALVFGNETFGLSIEEVRACNRLMTINGNPDYFSLNLAQAV 183 Query: 162 LLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLE 200 ++ +E + S ++++++ AT ++ L ++E Sbjct: 184 QVVCYEIF-SQTDSPMTHLQQEDHAATHEQIKGMLAHME 221 >3ilk_A Uncharacterized tRNA/RRNA methyltransferase HI0380; APC63004, methylase family protein, haemophilus influenzae RD KW20; 2.01A {Haemophilus influenzae} Length = 244 Score = 117 bits (293), Expect = 3e-27 Identities = 70/244 (28%), Positives = 124/244 (50%), Gaps = 12/244 (4%) Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76 I+L++ NIG ARAM LTQL LV+P+ E++ + SA A+ ++ + RV + Sbjct: 10 IVLIETSHSGNIGSAARAMKTMGLTQLCLVSPKS--VDEQSYALSAGAENIVKNARVVDS 67 Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEE 136 EA+ D + T+AR R+ +++ P + + + I+FGRER GLTNEE Sbjct: 68 FDEAVDDCSLVIGTSARLRHLQNTLIEP---RECAEKVVAYKGKIAIVFGRERIGLTNEE 124 Query: 137 IALSNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEK---NVKEQNTPATKGELL 193 + + ++ P NP + SLN++ AV L+ +E +V + K + T +L Sbjct: 125 LLKCHYHLNIPANPDYSSLNLAMAVQLVSYELRMAFLVQNNKKNSLSLIEKNYPTTDQLA 184 Query: 194 SFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRGIVSTLDKFSRQS 253 F DY E + G+ + + ++ L ++ R +L + E+ +L G++S ++K + Sbjct: 185 YFFDYTERIYQSLGFI----QNQGVMRKLKRLYYRAKLEKNELNILNGMLSAVEKRIDLT 240 Query: 254 SRRN 257 N Sbjct: 241 KEDN 244 >3dcm_X AdoMet, uncharacterized protein TM_1570; trefoil knot, spout mtase, adoMet binding, transferase; HET: SAM; 2.00A {Thermotoga maritima} Length = 192 Score = 107 bits (267), Expect = 3e-24 Identities = 21/163 (12%), Positives = 51/163 (31%), Gaps = 12/163 (7%) Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDG-----------WPSEKARSSSANAD 65 I+ ++ +AR +NL +V W + + Sbjct: 20 SIISTAVTNLDVHDIARTARTYNLKGYYIVTNLRAQQDMVSKMLKFWREGFGSRYNPSRA 79 Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125 + V++ S L++ + D+ + + I + +I Sbjct: 80 ESLKLVKLKSYLEDVLEDIESVEGERPLIFFTSAKKRENDISFEEGRRIIIETEKPVLIL 139 Query: 126 GRERWGLTNEEIALSNAIISF-PVNPLFPSLNISQAVLLMVWE 167 WGL +E + +S+ ++ F L++ A +++ Sbjct: 140 LGTGWGLPDEILEISDYVLEPIRAQSDFNHLSVRAAAAIIIDR 182 >3kty_A Probable methyltransferase; alpha-beta-alpha sandwich, structural genomics, PSI-2, protein structure initiative; 2.30A {Bordetella pertussis} Length = 173 Score = 98.8 bits (245), Expect = 1e-21 Identities = 51/164 (31%), Positives = 78/164 (47%), Gaps = 4/164 (2%) Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPR--DGWPSEKARSSSANAD 65 + + I+ P N+G ARA+ +L LV PR D +A + ++ A Sbjct: 4 MTQAFSRVRFIMTQPSHPGNVGSAARAIKTMGFGELVLVAPRFPDMTAQPEAVALASGAL 63 Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSG--QNVGI 123 V++ V L+EA+A + +A T R R+ +EAA + + V I Sbjct: 64 DVLERAAVHDTLEEALAPVTLAFALTTRVRDLGPPPCDIREAAGLARRHLDDTEAGVVAI 123 Query: 124 IFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167 + G ER GLTN +I L + I P NP + SLN++QA+ L WE Sbjct: 124 VLGTERAGLTNAQIELCHRICHIPANPQYSSLNVAQALQLAAWE 167 >1gz0_A Hypothetical tRNA/RRNA methyltransferase YJFH; 2'O-methyltransferase, knot, montreal- kingston bacterial structural genomics initiative, BSGI; 2.5A {Escherichia coli} SCOP: c.116.1.1 d.79.3.3 Length = 253 Score = 73.7 bits (180), Expect = 4e-14 Identities = 26/161 (16%), Positives = 55/161 (34%), Gaps = 11/161 (6%) Query: 7 QLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADC 66 + + + ++IL N+G R+ + + + R + A+ + A Sbjct: 98 LIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVACGAAE 157 Query: 67 VIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFG 126 + +RV +NL + L L + + ++ G Sbjct: 158 SVPLIRV-TNLARTMRMLQEENIWIVGTAGEADHTL----------YQSKMTGRLALVMG 206 Query: 127 RERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167 E G+ + +IS P+ SLN+S A + ++E Sbjct: 207 AEGEGMRRLTREHCDELISIPMAGSVSSLNVSVATGICLFE 247 >3n4j_A RNA methyltransferase; center for structural genomics of INF diseases, csgid; 1.47A {Yersinia pestis} PDB: 3n4k_A* 1mxi_A* 1j85_A* Length = 165 Score = 73.6 bits (180), Expect = 4e-14 Identities = 30/155 (19%), Positives = 55/155 (35%), Gaps = 10/155 (6%) Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76 I+L +P++ N G + R N QL L+ P +K + ++ + Sbjct: 7 IVLFEPEIPPNTGNIIRLCANTGC-QLHLIKPLGFTWDDKRLRRAGLDYHEFADIKHHHD 65 Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEE 136 + + AR + A + + N ++FG E GL Sbjct: 66 YQAFLDSEKLDSTQPAR-------LFALTTKGTPAHSAVSYQANDYLLFGPETRGLPAYI 118 Query: 137 IALSN--AIISFPVNPLFPSLNISQAVLLMVWECM 169 + I P+ S+N+S AV ++V+E Sbjct: 119 LDALPAQQKIRIPMQADSRSMNLSNAVSVVVYEAW 153 >1mxi_A YIBK, hypothetical tRNA/RRNA methyltransferase HI0766; S-adenosylhomocysteine, SPOU family, structure 2 function project; HET: SAH; 1.70A {Haemophilus influenzae} SCOP: c.116.1.1 PDB: 1j85_A* Length = 160 Score = 70.2 bits (171), Expect = 5e-13 Identities = 24/155 (15%), Positives = 50/155 (32%), Gaps = 15/155 (9%) Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76 I+L +P++ +N G + R N +L L+ P +K S ++ Sbjct: 4 IVLYEPEIPQNTGNIIRLCANTGF-RLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKT 62 Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE- 135 + + + + ++ ++FG E G+ Sbjct: 63 FEAFLESEKPKRLFALTTKGCPA------------HSQVKFKLGDYLMFGPETRGIPMSI 110 Query: 136 -EIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 I P+ S+N+S +V + V+E Sbjct: 111 LNEMPMEQKIRIPMTANSRSMNLSNSVAVTVYEAW 145 >3e5y_A TRMH family RNA methyltransferase; ssgcid, protein knot, decode, structural genomics; 2.40A {Burkholderia pseudomallei 305} Length = 160 Score = 66.9 bits (162), Expect = 5e-12 Identities = 27/155 (17%), Positives = 45/155 (29%), Gaps = 13/155 (8%) Query: 17 IILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFSN 76 ++LV+P++ N G V R N + K R + + Sbjct: 8 VVLVEPEIPPNTGNVIRLCANTGARLHLIEPLGFPLDDAKMRRAGLDYHEYAQMRVHRDW 67 Query: 77 LKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEE 136 A A + + A +FG E GL Sbjct: 68 -----------DAFVAAEAPDPARMFAFTTRGSGRFHDRAFEPGDWFVFGAETRGLAPAL 116 Query: 137 IALSNA--IISFPVNPLFPSLNISQAVLLMVWECM 169 + + P+ P SLN+S V ++V+E Sbjct: 117 VDRFAPEQRVRLPMRPGNRSLNLSNTVAVVVFEAW 151 >3nk6_A 23S rRNA methyltransferase; nosiheptide, nosiheptide-resistance methyltransferase, 23S R methyltransferase; 2.00A {Streptomyces actuosus} PDB: 3nk7_A* 3gyq_A* Length = 277 Score = 65.8 bits (160), Expect = 1e-11 Identities = 24/155 (15%), Positives = 56/155 (36%), Gaps = 10/155 (6%) Query: 13 KGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVR 72 G V++L ++ NIG + R + LV+ +++ ++ Sbjct: 118 GGDVVVLDGVKIVGNIGAIVRTSLALGAAGIVLVDSDLATIADRRLLRASRGYVFSL--- 174 Query: 73 VFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGL 132 + A + N+ ++ + + + + + ++FG E+ G Sbjct: 175 -------PVVLADREEAVSFLRDNDIALMVLDTDGDLGVKDLGDRADRMALVFGSEKGGP 227 Query: 133 TNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWE 167 + S +S P+ SLN+S +V + + E Sbjct: 228 SGLFQEASAGTVSIPMLSSTESLNVSVSVGIALHE 262 >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} SCOP: c.116.1.1 d.79.3.3 Length = 274 Score = 64.5 bits (156), Expect = 2e-11 Identities = 27/164 (16%), Positives = 56/164 (34%), Gaps = 13/164 (7%) Query: 6 PQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANAD 65 + + S +++ V + N+G V R+ + + D + + R+S+ Sbjct: 108 EEYRPSPDALILVAVGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQVIRNSTGVVF 167 Query: 66 CVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIF 125 + S + + I + T + A L V I Sbjct: 168 SLRTLAASESEVLDWIKQHNLPLVATTPH-------------AEALYWEANLRPPVAIAV 214 Query: 126 GRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 G E GL + + + P+ SLN+S + L+++E + Sbjct: 215 GPEHEGLRAAWLEAAQTQVRIPMQGQADSLNVSVSAALLLYEAL 258 >1zjr_A TRNA (guanosine-2'-O-)-methyltransferase; methylase, RNA modifying enzyme, topological knot; 1.85A {Aquifex aeolicus} Length = 211 Score = 61.7 bits (149), Expect = 1e-10 Identities = 20/162 (12%), Positives = 60/162 (37%), Gaps = 11/162 (6%) Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67 L+ K ++ + + N + R + L + +G ++ + + Sbjct: 19 LEKRQKDLIVFADNVKNEHNFSAIVRTCDAVGVLYLYYYHA-EGKKAKINEGITQGSHKW 77 Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127 + +V + +++ + + + A + + + ++ G Sbjct: 78 VFIEKVDNPVQKLLEFKNRGFQIVATWLSKESVN----------FREVDYTKPTVLVVGN 127 Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 E G++ E + +++ I P+ + SLN+S A ++++E Sbjct: 128 ELQGVSPEIVEIADKKIVIPMYGMAQSLNVSVATGIILYEAQ 169 >1x7o_A Avirb, rRNA methyltransferase; SPOU, C-terminal knot, seMet; 2.37A {Streptomyces viridochromogenes} PDB: 1x7p_A* Length = 287 Score = 57.7 bits (138), Expect = 2e-09 Identities = 24/154 (15%), Positives = 47/154 (30%), Gaps = 6/154 (3%) Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCVIDSVRVFS 75 ++ P NIG + R+ L + K + S+ Sbjct: 128 GVLFDRPTSPGNIGSIIRSADALGAHGLIVAGHAADVYDPK------SVRSSTGSLFSLP 181 Query: 76 NLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNE 135 ++ + R ++ E Q ++ G E GL+N Sbjct: 182 AVRVPSPGEVMDWVEARRAAGTPIVLVGTDEHGDCDVFDFDFTQPTLLLIGNETAGLSNA 241 Query: 136 EIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 L + +S P+ SLN + A +++E + Sbjct: 242 WRTLCDYTVSIPMAGSASSLNAANAATAILYEAV 275 >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} Length = 184 Score = 56.5 bits (135), Expect = 7e-09 Identities = 24/165 (14%), Positives = 52/165 (31%), Gaps = 9/165 (5%) Query: 5 APQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANA 64 A +L S +++ N+G + R F + L + + + + S + Sbjct: 17 AARLGKSISRLIVVASLIDKPTNLGGLCRTCEVFGASVLVVGSLQCISDKQFQHLSVSAE 76 Query: 65 DCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGII 124 + L + + T K + + + ++ Sbjct: 77 QWLPLVEVKPPQLIDYLQQKKTEGYTIIGVEQTAK---------SLDLTQYCFPEKSLLL 127 Query: 125 FGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 G ER G+ I + + P + SLN+ + L++WE Sbjct: 128 LGNEREGIPANLIQQLDVCVEIPQQGIIRSLNVHVSGALLIWEYT 172 >1v2x_A TRNA (GM18) methyltransferase; DEEP trefoil knot, riken structural genomics/proteomics initiative, RSGI, structural genomics; HET: SAM; 1.50A {Thermus thermophilus} SCOP: c.116.1.1 Length = 194 Score = 53.4 bits (127), Expect = 6e-08 Identities = 27/162 (16%), Positives = 54/162 (33%), Gaps = 12/162 (7%) Query: 8 LQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSANADCV 67 L+ ++L + N+ + R + + VNP G P Sbjct: 16 LRRRQPDLTVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPTGGVP------------TF 63 Query: 68 IDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGR 127 ++ A F + + ++FG Sbjct: 64 NETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTAVLFGA 123 Query: 128 ERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 E+WG++ E +AL++ I P+ + SLN+S A ++++E Sbjct: 124 EKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILFEAQ 165 >3gyq_A RRNA (adenosine-2'-O-)-methyltransferase; rRNA methyltransferase, spout mtases, SAM, trefoil knot, antibiotic resistance; HET: SAM; 2.45A {Streptomyces cyaneus} Length = 272 Score = 50.7 bits (120), Expect = 3e-07 Identities = 28/169 (16%), Positives = 61/169 (36%), Gaps = 10/169 (5%) Query: 1 MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSS 60 P S +G V++L ++ NIG + R + + LV+ + Sbjct: 106 PRPARFGDIASRRGDVVVLDGVKIVGNIGAIVRTSLALGASGIILVDSDITSIA------ 159 Query: 61 SANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQN 120 D + + A + + + + I + E + Sbjct: 160 ----DRRLQRASRGYVFSLPVVLSGREEAIAFIRDSGMQLMTLKADGDISVKELGDNPDR 215 Query: 121 VGIIFGRERWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLMVWECM 169 + ++FG E+ G ++ S+A +S P+ SLN+S ++ + + E + Sbjct: 216 LALLFGSEKGGPSDLFEEASSASVSIPMMSQTESLNVSVSLGIALHERI 264 >2i6d_A RNA methyltransferase, TRMH family; stuctural genomics, knot, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.85A {Porphyromonas gingivalis W83} Length = 257 Score = 43.9 bits (102), Expect = 4e-05 Identities = 25/172 (14%), Positives = 54/172 (31%), Gaps = 14/172 (8%) Query: 1 MTPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARSS 60 + + + +G ++L Q N+G + R F + + L S K + Sbjct: 90 VFDLPAEPEPVVEGLTLLLDGVQDPGNVGTILRTADWFGIRHVWLGTGSADVFSPKVVQA 149 Query: 61 SANADCVIDSVRVFSNLKEAIADLHFIYATTARNRNNFKSVLAPKEAAIVLNERIFSGQN 120 S A + + + R + ++ + Sbjct: 150 SMGALARVQPTPLKN---------TVDTLAYFRRQGIPVYGAFLDGQSLYEAPLPNFTEP 200 Query: 121 VGIIFGRERWGLTNEEIALSNAIISFPVNPL-----FPSLNISQAVLLMVWE 167 ++ G E G++ E A ++ P + L SLN++ A ++ E Sbjct: 201 AILVLGSEGRGISPEVAAEITDRLTIPASGLSVKGHTESLNVAIATAILCSE 252 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 2006 Score = 41.9 bits (98), Expect = 2e-04 Identities = 24/133 (18%), Positives = 45/133 (33%), Gaps = 31/133 (23%) Query: 139 LSNAII--SFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELL-SF 195 LS+ + V P+ + A L E + + + P T EL+ F Sbjct: 11 LSHGSLEHVLLV----PTASFFIASQL--QEQFNKILPEPTEGFAADDEPTTPAELVGKF 64 Query: 196 LDYLEISLEE--RGYFRPVEKKKKMLDDLYSIFIRPELMREEVFLLRG-----IVSTLDK 248 L Y+ +E G F V L+ + F E + L G + + L + Sbjct: 65 LGYVSSLVEPSKVGQFDQV------LNLCLTEF-------ENCY-LEGNDIHALAAKLLQ 110 Query: 249 FSRQS-SRRNNVL 260 + + + ++ Sbjct: 111 ENDTTLVKTKELI 123 Score = 41.1 bits (96), Expect = 3e-04 Identities = 34/204 (16%), Positives = 64/204 (31%), Gaps = 66/204 (32%) Query: 25 GENIGMVARAMWNFNLTQLRLVNP----------RDGWPSEKARSS----SANADCVIDS 70 G +I +A + N T L P +K +S + + Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEG----N 153 Query: 71 VRVFS------NLKEAIADLHFIYATTARNRNNFKSVLAP--KEAAIVLNERIFSGQNVG 122 ++ + N + +L +Y T + ++ K +A L+E I + + Sbjct: 154 AQLVAIFGGQGNTDDYFEELRDLYQT-------YHVLVGDLIKFSAETLSELIRTTLDAE 206 Query: 123 IIFGR----ERWGLTNEEIA-----LSNAIISFPVNPLFPSLNISQ-AVLLMVWECMENS 172 +F + W L N L + IS P+ + + ++ V + Sbjct: 207 KVFTQGLNILEW-LENPSNTPDKDYLLSIPISCPLIGV---IQLAHYVVTAKLLGF---- 258 Query: 173 IVSSEKNVKEQNTPATKGELLSFL 196 TP GEL S+L Sbjct: 259 ------------TP---GELRSYL 267 Score = 38.4 bits (89), Expect = 0.002 Identities = 39/268 (14%), Positives = 79/268 (29%), Gaps = 97/268 (36%) Query: 31 VARAMWNFNLTQLR------LVNPRDGWPSEKARSSSANADCVIDSVRVFSNLKEAIADL 84 V A + F +QL+ L P +G+ ++ ++ A E + Sbjct: 22 VPTASF-FIASQLQEQFNKILPEPTEGFAADDEPTTPA----------------ELVG-- 62 Query: 85 HFIYATTAR----NRNNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIALS 140 F+ ++ F VL + L E F E L +I Sbjct: 63 KFLGYVSSLVEPSKVGQFDQVL-----NLCLTE--F-----------ENCYLEGNDI--- 101 Query: 141 NAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPATKGELLSFLDYLE 200 +A+ + L + + + + + + +++ +++ A L + Sbjct: 102 HALAA----KLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSA----LFRAVGEGN 153 Query: 201 ISL----------EERGYFRPVEKKKKMLDDLYSI---FIRPELMREEVFLLRGIVSTLD 247 L ++ YF E L DLY + L++ TL Sbjct: 154 AQLVAIFGGQGNTDD--YFE--E-----LRDLYQTYHVLVGD--------LIKFSAETLS 196 Query: 248 KFSRQSSRRN-------NVL--LQKTEK 266 + R + N+L L+ Sbjct: 197 ELIRTTLDAEKVFTQGLNILEWLENPSN 224 Score = 36.1 bits (83), Expect = 0.008 Identities = 47/206 (22%), Positives = 75/206 (36%), Gaps = 73/206 (35%) Query: 87 IYATTAR-----NR--NNFKSVLAPKEAAIVLNERIFSGQNVGIIFGRERWGLTNEEIAL 139 +Y T+ NR N+FK IV+N + N+ I FG E+ E Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYGFSILDIVINNPV----NLTIHFGGEKGKRIRE---- 1686 Query: 140 SNAIISFPVNPLFPSLNISQAVLLMVWECMENSIVSSEKNVKEQNTPAT-------KGEL 192 N S M++E + + + +EK KE N +T KG L Sbjct: 1687 ----------------NYSA----MIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKG-L 1725 Query: 193 LSFLDYLE--ISLEERGYFRPVEKKKKM-------------------LDDLYSIFIRPEL 231 LS + + ++L E+ F ++ K + L D+ SI E Sbjct: 1726 LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVMSI----ES 1781 Query: 232 MREEVFLLRGIVSTL----DKFSRQS 253 + E VF RG+ + D+ R + Sbjct: 1782 LVEVVF-YRGMTMQVAVPRDELGRSN 1806 Score = 31.1 bits (70), Expect = 0.26 Identities = 23/137 (16%), Positives = 43/137 (31%), Gaps = 47/137 (34%) Query: 2 TPYAPQLQNSAKGPVIILVDPQLGENIGMVARAMWNFNLTQLRLVNP----RDGWPSEKA 57 + L ++ +I D + + +FN +++ P DG Sbjct: 429 SHL---LVPASD---LINKD---------LVKNNVSFNAKDIQI--PVYDTFDG---SDL 468 Query: 58 RSSSANADCVIDSVRVFSNLKEAIADL--HFIYATTARNRNNFKS----VLAPKEAA-I- 109 R S + + + + + I L + T FK+ P A+ + Sbjct: 469 RVLSGS---ISER------IVDCIIRLPVKWETTT------QFKATHILDFGPGGASGLG 513 Query: 110 VLNERIFSGQNVGIIFG 126 VL R G V +I Sbjct: 514 VLTHRNKDGTGVRVIVA 530 >1pvv_A Otcase, ornithine carbamoyltransferase; dodecamer; 1.87A {Pyrococcus furiosus} SCOP: c.78.1.1 c.78.1.1 PDB: 1a1s_A Length = 315 Score = 32.0 bits (72), Expect = 0.15 Identities = 15/85 (17%), Positives = 28/85 (32%), Gaps = 4/85 (4%) Query: 16 VIILVDPQLGENIGMVARAMWNFNLTQLRLVNPRDGWPSEKARS-SSANADCVIDSVRVF 74 V+ + D + M+A ++ + P P EK + NA S + Sbjct: 158 VVYVGDGNNVAHSLMIAGTKLGADV---VVATPEGYEPDEKVIKWAEQNAAESGGSFELL 214 Query: 75 SNLKEAIADLHFIYATTARNRNNFK 99 + +A+ D IY + Sbjct: 215 HDPVKAVKDADVIYTDVWASMGQEA 239 >2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D Length = 1524 Score = 30.1 bits (67), Expect = 0.48 Identities = 15/73 (20%), Positives = 26/73 (35%) Query: 170 ENSIVSSEKNVKEQNTPATKGELLSFLDYLEISLEERGYFRPVEKKKKMLDDLYSIFIRP 229 IV K P K +LL+ +Y E+ ++ + ++ D + Sbjct: 130 SKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQ 189 Query: 230 ELMREEVFLLRGI 242 EL V L G+ Sbjct: 190 ELAPGVVSRLDGV 202 >1jjv_A Dephospho-COA kinase; P-loop nucleotide-binding fold, structure 2 function project, S2F, structural genomics, transferase; HET: ATP; 2.00A {Haemophilus influenzae} SCOP: c.37.1.1 Length = 206 Score = 28.9 bits (64), Expect = 1.2 Identities = 23/102 (22%), Positives = 38/102 (37%), Gaps = 18/102 (17%) Query: 13 KGPVIILVDPQLGEN----IGMVARAMWNFNLTQLRLVNPRDGWPSEKARSSSAN----- 63 P + V P L EN + + TQL RD E+ + + Sbjct: 104 TAPYTLFVVPLLIENKLTALCDRILVVDVSPQTQLARSAQRDNNNFEQIQRIMNSQVSQQ 163 Query: 64 -----ADCVIDS----VRVFSNLKEAIADLHFIYATTARNRN 96 AD VI++ + +L++ + +LH Y A N+N Sbjct: 164 ERLKWADDVINNDAELAQNLPHLQQKVLELHQFYLQQAENKN 205 >1t7r_A Androgen receptor; nuclear receptor, transcription factor, ligand binding domain, AF-2, androgen, testosterone, DHT, alpha-helical sandwich; HET: DHT; 1.40A {Pan troglodytes} SCOP: a.123.1.1 PDB: 1t73_A* 1t76_A* 1t74_A* 1t79_A* 1t7m_A* 1t7f_A* 1t7t_A* 2am9_A* 2ama_A* 2amb_A* 2pnu_A* 1e3g_A* 2q7i_A* 1xj7_A* 2q7j_A* 3g0w_A* 2ihq_A* 2nw4_A* 1i37_A* 2q7k_A* ... Length = 269 Score = 27.7 bits (61), Expect = 3.0 Identities = 17/118 (14%), Positives = 36/118 (30%), Gaps = 28/118 (23%) Query: 129 RWGLTNEEIALSNAIISFPVNPLFPSLNISQAVLLM---VWECMENSIVSSEKNVKEQNT 185 +T +E A++ F L + + + ++ I KN Sbjct: 146 WLQITPQEFLCMKALLLFS-IIPVDGLKNQKFFDELRMNYIKELDRIIACKRKNPTSC-- 202 Query: 186 PATKGELLSFLDYL-EISLEERGYFRPVEKKKKMLDDLYSIFIR--------PELMRE 234 +L LD + I+ +++ + + I+ PE+M E Sbjct: 203 SRRFYQLTKLLDSVQPIA-------------RELHQFTFDLLIKSHMVSVDFPEMMAE 247 >2k3i_A Uncharacterized protein YIIS; GFT protein structure, PSI, NESG, structural genomics, protein structure initiative; NMR {Shigella flexneri 2A} Length = 109 Score = 27.1 bits (60), Expect = 4.8 Identities = 15/70 (21%), Positives = 25/70 (35%), Gaps = 8/70 (11%) Query: 63 NADCVIDSVRVFSNLKEAIADLHFIYATTARNRN------NFKSVLAPKEAAIVLNERI- 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 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 0.318 0.133 0.380 Gapped Lambda K H 0.267 0.0535 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,178,967 Number of extensions: 98632 Number of successful extensions: 270 Number of sequences better than 10.0: 1 Number of HSP's gapped: 251 Number of HSP's successfully gapped: 31 Length of query: 268 Length of database: 5,693,230 Length adjustment: 91 Effective length of query: 177 Effective length of database: 3,487,026 Effective search space: 617203602 Effective search space used: 617203602 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: 56 (25.8 bits)