RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|255764510|ref|YP_003065448.2| uroporphyrinogen-III synthase [Candidatus Liberibacter asiaticus str. psy62] (232 letters) >3mw8_A Uroporphyrinogen-III synthase; structural genomics, joint center for structural genomics, J protein structure initiative, PSI-2, lyase; 1.65A {Shewanella amazonensis} Length = 240 Score = 86.4 bits (213), Expect = 6e-18 Identities = 33/240 (13%), Positives = 73/240 (30%), Gaps = 11/240 (4%) Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFIHDRES-VFLAMQQSYGAIAITSSES 59 M +++TRP K + + ++ PL + L + S+ + Sbjct: 2 MKLLLTRPEGKNAAMASALDALAIPYLVEPLLSVEAAAVTQAQLDELSRADILIFISTSA 61 Query: 60 LSTLPANFCR---HTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKIIVEQKVLFTPQ 116 +S +A+G+A+A +G T D+ + + + + Sbjct: 62 VSFATPWLKDQWPKATYYAVGDATADALALQGITAERSPADSQATEGLLTLPSLEQVSGK 121 Query: 117 KPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQNA--DAILFYA 174 + +I G R D L + ++ Y + Q+ D I+ + Sbjct: 122 QIVIVRGKGGREAM-ADGLRLRGANVSYLEVYQRACPPLDAPASVSRWQSFGIDTIVVTS 180 Query: 175 RSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVVTVACFPKETSLLKLLPL 230 + +L + S + + VT A + ++L L + Sbjct: 181 GEVLENLINLVPKDSFAWLRDCHIIVPSARVETQARKKGLRRVTNAGAANQAAVLDALGM 240 >1jr2_A Uroporphyrinogen-III synthase; heme biosynthesis, HEAM biosynthesis, lyase; 1.84A {Homo sapiens} SCOP: c.113.1.1 Length = 286 Score = 72.5 bits (177), Expect = 8e-14 Identities = 36/255 (14%), Positives = 77/255 (30%), Gaps = 32/255 (12%) Query: 3 IVITRPIKKAL---RTQEKIQKMGYIPVMMPL---SYFIHDRESVFLAMQQSYGAIAITS 56 +++ + ++ G ++P+ + S L+ + YG + TS Sbjct: 25 LLLKDAKEDDCGQDPYIRELGLYGLEATLIPVLSFEFLSLPSFSEKLSHPEDYGGLIFTS 84 Query: 57 SESLSTL----------------PANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNSI 100 ++ ++ +G A+A L + G N+ Sbjct: 85 PRAVEAAELCLEQNNKTEVWERSLKEKWNAKSVYVVGNATASLVSKIGLDTEGETCGNAE 144 Query: 101 NLAKIIVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTM 160 LA+ I ++ PL++ G + L + I + I Y + + + Sbjct: 145 KLAEYICSRES---SALPLLFPCGNLKREILPKALKDKGIAMESITVYQTVAHPGIQGNL 201 Query: 161 KNLLQNA---DAILFYARSSVLYFFSL----PLPAKISAAFLCLSNNIASAIPASYKNVV 213 + +I F++ S + Y F + A A+ A V Sbjct: 202 NSYYSQQGVPASITFFSPSGLTYSLKHIQELSGDNIDQIKFAAIGPTTARALAAQGLPVS 261 Query: 214 TVACFPKETSLLKLL 228 A P +L + Sbjct: 262 CTAESPTPQALATGI 276 >3p9z_A Uroporphyrinogen III cosynthase (HEMD); MCSG, PSI2, structural genomics, protein structure initiativ midwest center for structural genomics; HET: MSE; 2.10A {Helicobacter pylori} Length = 229 Score = 59.7 bits (144), Expect = 6e-10 Identities = 32/190 (16%), Positives = 64/190 (33%), Gaps = 14/190 (7%) Query: 48 SYGAIAITSSES--------LSTLPANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNS 99 + A+ TS + ++ ++ P +A+ E +A + F F G+ Sbjct: 37 PFNALIFTSKNAVFSLLETLKNSPKLKMLQNIPAYALSEPTAKTLQDHHFKVAFMGEKAH 96 Query: 100 INLAKIIVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETT 159 K V++ +K ++YL K + L+EH I + Y ++ + Sbjct: 97 ---GKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSE 153 Query: 160 MKNLLQN-ADAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNVVTVACF 218 L ++F A S F + + + N A + +A Sbjct: 154 QNALKPKEKSILIFTAISHAKAFLHY-FEFLENYTAISIGNTTALYLQEQGIPSY-IAKK 211 Query: 219 PKETSLLKLL 228 P + L+L Sbjct: 212 PSLEACLELA 221 >1wcw_A Uroporphyrinogen III synthase; congenital erythropoietic porphyria, structural genomics, riken structural genomics/proteomics initiative; 1.30A {Thermus thermophilus} PDB: 1wd7_A 1wcx_A Length = 261 Score = 50.4 bits (120), Expect = 3e-07 Identities = 34/244 (13%), Positives = 70/244 (28%), Gaps = 27/244 (11%) Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYF----IHDRESVFLAMQQSYGAIAITS 56 + + ++ + +K+G+ P++ P+ + + A+ Q T+ Sbjct: 9 VRVAYAGL-RRKEAFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRALAQGVDLFLATT 67 Query: 57 SESLSTL----------PANFCRHTPIFAIGEASACLARQKGFTQIFHGKDNSINLAKII 106 + L A G +A ++ G G S +L ++ Sbjct: 68 GVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLL 127 Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYPETTMKNLLQN 166 + + + L GKP E+ L E + + Y ++ L Sbjct: 128 PQGR-----GVAALQLYGKPLPL-LENALAERGYRVLPLMPYRHLPDPEGILRLEEALLR 181 Query: 167 A--DAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNV----VTVACFPK 220 DA+ F A V + F K L + + + V + Sbjct: 182 GEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDE 241 Query: 221 ETSL 224 L Sbjct: 242 TERL 245 >3d8t_A Uroporphyrinogen-III synthase; heme biosynthesis, lyase; 1.60A {Thermus thermophilus} PDB: 3d8r_A 3d8s_A 3d8n_A Length = 286 Score = 48.1 bits (114), Expect = 2e-06 Identities = 36/244 (14%), Positives = 67/244 (27%), Gaps = 27/244 (11%) Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLS--YFIHDRESVFLAMQ--QSYGAIAITS 56 M I ++ + +K+G+ P++ P+ + E + Q T+ Sbjct: 34 MRIAYAGL-RRKEEFKALAEKLGFTPLLFPVQATEKVPVPEYRDQVRELAQGVDLFLATT 92 Query: 57 SESLSTLPANFCRH----------TPIFAIGEASACLARQKGFTQIFHGKDNSINLAKII 106 + L A G +A ++ G G S +L ++ Sbjct: 93 GVGVRDLLEAGKALGLDLEGPLAKAFRLARGAKAARALKEAGLPPHAVGDGTSKSLLPLL 152 Query: 107 VEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYYSQDIAYP--ETTMKNLL 164 + + + L GKP E+ L E + + Y L Sbjct: 153 PQGR-----GVAALQLYGKPLPL-LENALAERGYRVLPLMPYRHLPDPEGILRLEEAVLR 206 Query: 165 QNADAILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNV----VTVACFPK 220 DA+ F A V + F K L + + + V + Sbjct: 207 GEVDALAFVAAIQVEFLFEGAKDPKALREALNTRVKALAVGRVTADALREWGVKPFYVDE 266 Query: 221 ETSL 224 L Sbjct: 267 TERL 270 >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 = 33.8 bits (77), Expect = 0.031 Identities = 44/271 (16%), Positives = 76/271 (28%), Gaps = 105/271 (38%) Query: 9 IKKALRTQEKIQKMGY---IPVMMPL-------SYFI-------HDRESVFLAMQQ---- 47 I + L Y IP+ PL Y + E ++ Sbjct: 215 ILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGE-----LRSYLKG 269 Query: 48 ----SYG---AIAITSSESLSTLPANFCRHTPI---FAIGEASACLARQKGFTQIFHGKD 97 S G A+AI ++S + + I F IG + + Sbjct: 270 ATGHSQGLVTAVAIAETDSWESFFVSV--RKAITVLFFIGVRC-----YEAYPNTS---- 318 Query: 98 NSINLAKIIVEQKV---LFTPQKPLIYLGGKPRNFHFEDYLIEHKIPLRVID---CYYSQ 151 L I+E + P P++ + + + + ++ ++ + Sbjct: 319 ----LPPSILEDSLENNEGVPS-PMLSISNLTQ-----EQVQDY------VNKTNSHLPA 362 Query: 152 D----IAYPETTMKNLLQNADAILFYARSSV-------LYFFSLPLPAKISAAFLCLSNN 200 I+ L N A++ V LY +L L K A S Sbjct: 363 GKQVEIS---------LVNG------AKNLVVSGPPQSLYGLNLTL-RKAKAP----SGL 402 Query: 201 IASAIPASYKNVVTVACF-----PKETSLLK 226 S IP S + + F P + LL Sbjct: 403 DQSRIPFSERKLKFSNRFLPVASPFHSHLLV 433 Score = 31.5 bits (71), Expect = 0.16 Identities = 31/208 (14%), Positives = 56/208 (26%), Gaps = 63/208 (30%) Query: 48 SYGAIAIT------SSESLSTLPANFCRH----TPIFAIGEASAC----LARQKGFTQIF 93 S+G++ S S L F + T FA + + + G+ Sbjct: 12 SHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAELVGKFLGYV-SS 70 Query: 94 HGKDNSINLAKIIVEQKVL--FTPQKPLIYLGGKPRNFH--FEDYLIEHKIPL----RVI 145 + + + ++ L F YL G + H L E+ L +I Sbjct: 71 LVEPSKVGQFDQVL-NLCLTEFENC----YLEGN--DIHALAAKLLQENDTTLVKTKELI 123 Query: 146 DCYY-----SQDIAYPETTMKNLLQNA---DAILFYARSSVL--------YFFSL----- 184 Y ++ + + + L + +A L A + YF L Sbjct: 124 KNYITARIMAKR-PFDKKSNSALFRAVGEGNAQL-VA---IFGGQGNTDDYFEELRDLYQ 178 Query: 185 -------PLPAKISAAFLCLSNNIASAI 205 L + L A Sbjct: 179 TYHVLVGDLIKFSAETLSELIRTTLDAE 206 >2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} Length = 1688 Score = 29.0 bits (64), Expect = 0.86 Identities = 38/183 (20%), Positives = 69/183 (37%), Gaps = 33/183 (18%) Query: 38 RESVFLAMQQSYGAIAITSSESLSTLPANFCRHTPIFAIGEASACLARQKGFTQIFHGKD 97 +ES M + I+SS + T P C A++ + G I GK Sbjct: 1077 QESFINTMSAWVNMLLISSSGPIKT-PVGAC----------ATSVESVDIGVETILSGK- 1124 Query: 98 NSINLAKI-IVEQKVLFTPQKPLIYLGGKPRNFHFEDYLIEH-KIPLRVIDCYYSQDIAY 155 A+I IV F + + K + E++ EH + P +++ Sbjct: 1125 -----ARICIVGGYDDFQEEGSFEFGNMKATSNTLEEF--EHGRTP---------AEMSR 1168 Query: 156 PETTMKNLLQNADA--ILFYARSSVLYFFSLPLPAKISAAFLCLSNNIASAIPASYKNVV 213 P TT +N A I ++ + +P+ ++ A ++ I ++PA K ++ Sbjct: 1169 PATTTRNGFMEAQGAGIQIIMQADLALKMGVPIYGIVAMA-ATATDKIGRSVPAPGKGIL 1227 Query: 214 TVA 216 T A Sbjct: 1228 TTA 1230 >2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1 PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C* 2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C 1l9z_C 1i6v_C* Length = 1119 Score = 27.8 bits (61), Expect = 2.4 Identities = 9/35 (25%), Positives = 15/35 (42%) Query: 1 MYIVITRPIKKALRTQEKIQKMGYIPVMMPLSYFI 35 +Y + K +E +G+IP+M FI Sbjct: 94 LYARLQLIHKDTGLIKEDEVFLGHIPLMTEDGSFI 128 >1ivz_A Hypothetical protein 1110008I14RIK; structural genomics, SEA domain, mucin 16, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: d.58.41.1 Length = 132 Score = 26.3 bits (57), Expect = 6.2 Identities = 22/56 (39%), Positives = 26/56 (46%), Gaps = 9/56 (16%) Query: 149 YSQDIAYPETT----MKNLLQNADAILFYARSSVLYFFSLPLPAKISAAFLCLSNN 200 YSQDIA P TT K ++NA LF S YF + AF +SNN Sbjct: 25 YSQDIAQPSTTKYQQTKRSIENALNQLFRNSSIKSYFSDCQV-----LAFRSVSNN 75 >1tzf_A Glucose-1-phosphate cytidylyltransferase; nucleotidyltransferase, mixed alpha/beta fold; HET: C5G; 2.10A {Salmonella enterica subsp} SCOP: c.68.1.13 PDB: 1wvc_A* Length = 259 Score = 25.8 bits (55), Expect = 8.2 Identities = 12/33 (36%), Positives = 17/33 (51%) Query: 117 KPLIYLGGKPRNFHFEDYLIEHKIPLRVIDCYY 149 KP++ +GGKP +H H I +I C Y Sbjct: 25 KPMVEIGGKPILWHIMKMYSVHGIKDFIICCGY 57 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 0.138 0.405 Gapped Lambda K H 0.267 0.0530 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,874,483 Number of extensions: 79832 Number of successful extensions: 328 Number of sequences better than 10.0: 1 Number of HSP's gapped: 316 Number of HSP's successfully gapped: 15 Length of query: 232 Length of database: 5,693,230 Length adjustment: 89 Effective length of query: 143 Effective length of database: 3,535,514 Effective search space: 505578502 Effective search space used: 505578502 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: 55 (25.4 bits)