RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780628|ref|YP_003065041.1| coproporphyrinogen III oxidase [Candidatus Liberibacter asiaticus str. psy62] (395 letters) >1olt_A Oxygen-independent coproporphyrinogen III oxidase; heme biosynthesis, decarboxylase, radical SAM enzyme, 4Fe- 4S cluster; HET: SAM; 2.07A {Escherichia coli} SCOP: c.1.28.2 Length = 457 Score = 276 bits (707), Expect = 5e-75 Identities = 90/404 (22%), Positives = 168/404 (41%), Gaps = 21/404 (5%) Query: 5 SAYENNMTGQGSNSLGVYVHWPFCVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQ 64 A+ + L +YVH PFC K C +C N V R + + ++ + E+ Sbjct: 39 QAFLQAVARYPERPLSLYVHIPFCHKLCYFCGCNKIVTRQQHKADQYLDALEQEIVHRAP 98 Query: 65 LTGPRSISSIFFGGGTPSLIEPQNIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQG 124 L R +S + +GGGTP+ + I+ ++ + +N+ +++ EI+IE +P +E++ Sbjct: 99 LFAGRHVSQLHWGGGTPTYLNKAQISRLMKLLRENFQFNADAEISIEVDPREIELDVLDH 158 Query: 125 YRKAGVNRISLGVQSLEEQSLRFLGRNHNASEAIAAIHLARNI-FPRMSFDLIYALPKQT 183 R G NR+S+GVQ ++ R + R + A ++ AR I F + DLIY LPKQT Sbjct: 159 LRAEGFNRLSMGVQDFNKEVQRLVNREQDEEFIFALLNHAREIGFTSTNIDLIYGLPKQT 218 Query: 184 MTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYNLTQSIT 243 + L+R D LS++ T+F K D LPS +D+ T + Sbjct: 219 PESFAFTLKRVAELNPDRLSVFNYAHL-PTIFAAQRKIKDADLPSPQQKLDILQETIAFL 277 Query: 244 SAHGLHAY----------EISNHSFLGAESLHNLNYWRYGDYIGIGPGAHSRVKVGSHRV 293 + G E++ G + Y GD +G G + +G Sbjct: 278 TQSGYQFIGMDHFARPDDELAVAQREGVLHRNFQGYTTQGDTDLLGMGVSAISMIGDCY- 336 Query: 294 AISIEKHPESWLKMVRKNGHAVVEKEFLSSEQQADEFLMMGLRLREGISVKDWEMLAGRN 353 +K + + + V + G+A+ L+ + ++ L + E Sbjct: 337 -AQNQKELKQYYQQVDEQGNALWRGIALTRDDCIRRDVIKSLICNFRLDYSPIEQQWDLL 395 Query: 354 L------DIECERNLQRQGFIERVQFSRLRCTQRGMTMLDSVIA 391 D++ L + G ++ + ++ T +G ++ ++ Sbjct: 396 FADYFAEDLKLLAPLAKDGLVDVDE-KGIQVTAKGRLLIRNICM 438 >3iix_A Biotin synthetase, putative; adoMet radical, SAM radical, adoMet cleavage, Fe4S4 cluster, HYDE, hydrogenase, maturation, beta barrel; HET: OTY CSO 5AD CPS; 1.25A {Thermotoga maritima} PDB: 3ciw_A* 3iiz_A* 3cix_A* Length = 348 Score = 43.4 bits (101), Expect = 9e-05 Identities = 28/193 (14%), Positives = 56/193 (29%), Gaps = 12/193 (6%) Query: 28 CVKKCPYCDFNSHVRRYKVGQENFIQSFLTEMQWMRQLTGPRSISSIFFGGGTPSLIEPQ 87 C K C YC + E+ +L +I G P Sbjct: 63 CRKNCLYCGLRRD-----NKNLKRYRMTPEEIVERARLAVQFGAKTIVLQSGEDPYXMPD 117 Query: 88 NIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRF 147 I+ I+ I K + + ++ +++AG +R L ++ R Sbjct: 118 VISDIVKEIKKMGVAVTL-------SLGEWPREYYEKWKEAGADRYLLRHETANPVLHRK 170 Query: 148 LGRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLSLYQL 207 L + + + + + + + LP QT+ +L + D + + Sbjct: 171 LRPDTSFENRLNCLLTLKELGYETGAGSMVGLPGQTIDDLVDDLLFLKEHDFDMVGIGPF 230 Query: 208 TIEKGTLFYKMHK 220 T K Sbjct: 231 IPHPDTPLANEKK 243 >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 = 42.6 bits (100), Expect = 1e-04 Identities = 55/297 (18%), Positives = 88/297 (29%), Gaps = 121/297 (40%) Query: 49 ENFIQSFLTEMQ---WM--R-QLTGPR-SIS------SIFFGGGTPS------------- 82 E+F S + ++ R P S+ S+ G PS Sbjct: 290 ESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQV 349 Query: 83 --LIE------PQN----IALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGY----R 126 + P I+L+ +G AKN VS P S+ G R Sbjct: 350 QDYVNKTNSHLPAGKQVEISLV-NG-AKNLVVS--------GPPQSL-----YGLNLTLR 394 Query: 127 KAGV------NRISLGVQSLEEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYALP 180 KA +RI + L+ S RFL +A+ P F Sbjct: 395 KAKAPSGLDQSRIPFSERKLK-FSNRFL--------PVAS--------P---FHSHL--- 431 Query: 181 KQTMTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKM---H-KDG-DLVLPSENVAVDL 235 L A L ++ + ++ DG DL + S ++ Sbjct: 432 ----------LVPASDLINKDLVKNNVSFNAKDI--QIPVYDTFDGSDLRVLSGSI---S 476 Query: 236 YNLTQSITSAHGLHAYEISNHSFLGAESLHNLNYWRYGDYIGIGPGAHSRVKVGSHR 292 + I + +E + ++ H L D+ GPG S + V +HR Sbjct: 477 ERIVDCIIRLP-VK-WETT----TQFKATHIL------DF---GPGGASGLGVLTHR 518 Score = 39.9 bits (93), Expect = 9e-04 Identities = 65/378 (17%), Positives = 118/378 (31%), Gaps = 139/378 (36%) Query: 59 MQWMRQLTGPRSISSIFFGGGTP-SLIEPQNIALILDGIAK--NWTVSSNVEITIEANPS 115 ++W L P + + P S P LI G+ + ++ V++ + + P Sbjct: 216 LEW---LENPSNTPDKDYLLSIPISC--P----LI--GVIQLAHYVVTAKL---LGFTPG 261 Query: 116 SVEVN-NFQGYRKAGVNRISLGV------------QSLEEQSLR------FLG-RNHNAS 155 E+ +G G S G+ +S + F+G R + A Sbjct: 262 --ELRSYLKG--ATGH---SQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVRCYEA- 313 Query: 156 EAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRA-----LSYAVDHLSLYQL--T 208 +P S LP ++ + +E LS + +L+ Q+ Sbjct: 314 ------------YPNTS------LP-PSILEDSLENNEGVPSPMLS--ISNLTQEQVQDY 352 Query: 209 IEKGTLFYKMHKDGDLVLPSEN-VAVDLYNLTQSITSAHGLHAYEISNHSFLGAESLHNL 267 + K H LP+ V + L N +++ + G +SL+ L Sbjct: 353 VNK---TNS-H------LPAGKQVEISLVNGAKNLVVS-GP------------PQSLYGL 389 Query: 268 NYW-RYGDYIGIGPGA-HSRV-----KVG-SHR-VAISIEKHPESWLKMVRKNGHAVVEK 318 N R G SR+ K+ S+R + ++ H L ++ K Sbjct: 390 NLTLR---KAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFH-SHLLVPAS----DLINK 441 Query: 319 EFLSSEQQADEFLMMGLRLREGISVKDWEMLAGRNLDIECERNLQ--------RQGFIER 370 + + ++ I V D G +L R L Sbjct: 442 DL-----VKNNVSFNAKDIQ--IPVYDTF--DGSDL-----RVLSGSISERIVDCIIRLP 487 Query: 371 VQFSRLRCTQRGMT-MLD 387 V++ TQ T +LD Sbjct: 488 VKWE--TTTQFKATHILD 503 Score = 33.4 bits (76), Expect = 0.10 Identities = 36/210 (17%), Positives = 55/210 (26%), Gaps = 96/210 (45%) Query: 35 CDFNSHVRRYKVGQE-------------NFIQSFLTEMQWMRQLTGPRSISSIFFGGGTP 81 N +R+ K F FL P ++S F + Sbjct: 387 YGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFL-----------P--VASPFH---SH 430 Query: 82 SLIEPQNIALILDGIAKNWTVSSNVEITIEANPSSVEV-NNFQGYRKAGVNRISLGVQSL 140 L+ LI + KN ++ A + V + F G Sbjct: 431 LLVPAS--DLINKDLVKN-------NVSFNAKDIQIPVYDTFDG---------------- 465 Query: 141 EEQSLRFLGRNHNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVD 200 LR S +I R+ D I LP +WE + Sbjct: 466 --SDLR------VLSG---------SISERI-VDCIIRLP----VKWE----TTTQFKAT 499 Query: 201 HLSLYQLT--------IEKGTLFYKMHKDG 222 H+ L + G L ++ KDG Sbjct: 500 HI----LDFGPGGASGL--GVLTHRN-KDG 522 Score = 30.3 bits (68), Expect = 0.80 Identities = 44/223 (19%), Positives = 87/223 (39%), Gaps = 48/223 (21%) Query: 178 ALPKQTMTQWEMELQRALSYAVDHLSLYQLTIEKGTLFYKMHKDGDLVLPSENVAVDLYN 237 A+ +T+ +++ ++ +H + Y EKG L L L + DL + Sbjct: 1690 AMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKS 1749 Query: 238 L----TQSITSAHGLHAYE--ISNHSFLGAESLHNLNYWR-----------------YGD 274 + + H L Y S + ESL + ++R YG Sbjct: 1750 KGLIPADATFAGHSLGEYAALASLADVMSIESLVEVVFYRGMTMQVAVPRDELGRSNYG- 1808 Query: 275 YIGIGPGAHSRVKVGSHRVAISIEKHPESWL--KMVRKNGHAVVEKEFLSSEQQADEFLM 332 I I PG RVA S + ++ ++ ++ G V E ++ + +++ Sbjct: 1809 MIAINPG----------RVAASFSQEALQYVVERVGKRTGWLV---EIVNYNVENQQYVA 1855 Query: 333 MG-LRLREGIS-VKDWEMLAGRNLD-IECERNLQRQGFIERVQ 372 G LR + ++ V ++ L + +D IE +++L +E V+ Sbjct: 1856 AGDLRALDTVTNVLNFIKL--QKIDIIELQKSLS----LEEVE 1892 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 31.1 bits (69), Expect = 0.49 Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 19/46 (41%) Query: 141 EEQSLRFLGRNHNASEAIAAIHL-ARNIFPRMSFDLIYALP-KQTM 184 E+Q+L+ L AS + L A + P AL K TM Sbjct: 18 EKQALKKL----QAS-----LKLYADDSAP--------ALAIKATM 46 >2gzs_A IROE protein; enterobactin, salmochelin, DFP, hydrolase, catalytic DYAD; HET: DFP; 1.40A {Escherichia coli} SCOP: c.69.1.38 PDB: 2gzr_A* Length = 278 Score = 30.7 bits (68), Expect = 0.58 Identities = 10/133 (7%), Positives = 28/133 (21%), Gaps = 4/133 (3%) Query: 152 HNASEAIAAIHLARNIFPRMSFDLIYALPKQTMTQWEMELQRALSYAVDHLSLYQLTIEK 211 ++ + + + S+ + + L I + Sbjct: 147 GHSYGGLFVLDSWLSSSYFRSYYSASPSLGRGYDALLSRVTAVEPLQFCTKHLA---IME 203 Query: 212 GTLFYKMHKDGDLVLPSENVAVDLYNLTQSITSAHGLHAYEISNHSFLGAESLHNLNYWR 271 G+ +++ V + + + H + S Sbjct: 204 GSATQGDNRETHAVGVLSK-IHTTLTILKDKGVNAVFWDFPNLGHGPMFNASFRQALLDI 262 Query: 272 YGDYIGIGPGAHS 284 G+ G H Sbjct: 263 SGENANYTAGCHE 275 >3lyw_A YBBR family protein; structural genomics, PSI-2, protein structure initiative, northeast structural genomics consortium, NESG; 1.90A {Desulfitobacterium hafniense} PDB: 2kpu_A Length = 90 Score = 28.4 bits (63), Expect = 3.3 Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 8/61 (13%) Query: 88 NIALILDGIAKNWTVSS---NVEITIEANPSSVEVNNFQGY-----RKAGVNRISLGVQS 139 ++LI N + + +V + E S+ VN Y + G + + V+ Sbjct: 6 TLSLIAKNTPANSMIMTKLPSVRVKTEGYNPSINVNELFAYVDLSGSEPGEHDYEVKVEP 65 Query: 140 L 140 + Sbjct: 66 I 66 >1z3i_X Similar to RAD54-like; recombination ATPase helicase, recombination/DNA binding complex; 3.00A {Danio rerio} SCOP: c.37.1.19 c.37.1.19 Length = 644 Score = 26.9 bits (58), Expect = 7.8 Identities = 21/240 (8%), Positives = 58/240 (24%), Gaps = 10/240 (4%) Query: 156 EAIAAIHLARNIFPRMSFDLIYAL---PKQTMTQWEMELQRALSYAVDHLSLYQLTIEKG 212 + I I P ++ + P + W E+ + L V +++ + ++ Sbjct: 95 QCITLIWTLLKQSPDCKPEIDKVIVVSPSSLVRNWYNEVGKWLGGRVQPVAIDGGSKDEI 154 Query: 213 TLFYKMHKDGDLVLPSENVAVDLYNLTQSITSAHGLHAYEISNHSFLGAESLHNLNYWRY 272 + + + Y + + E N Sbjct: 155 DSKLVNFISQQGMRIPTPILIISYETFRLHAEVLHKGKVGLVICD----EGHRLKNSDNQ 210 Query: 273 GDYIGIGPGAHSRVKVGSHRVAISIEKHPESWLKM---VRKNGHAVVEKEFLSSEQQADE 329 A RV + + + ++ + + ++ + + D Sbjct: 211 TYLALNSMNAQRRVLISGTPIQNDLLEYFSLVHFVNSGILGTAQEFKKRFEIPILKGRDA 270 Query: 330 FLMMGLRLREGISVKDWEMLAGRNLDIECERNLQRQGFIERVQFSRLRCTQRGMTMLDSV 389 R +++ + R L L + ++ Q T + Sbjct: 271 DASDKDRAAGEQKLQELISIVNRCLIRRTSDILSKYLPVKIEQVVCCNLTPLQKELYKLF 330 >3en9_A Glycoprotease, O-sialoglycoprotein endopeptidase/protein kinase; endopeptidase activity, protein kinase activity; HET: TBR; 2.67A {Methanocaldococcus jannaschii} PDB: 3enh_A* 2vwb_A* Length = 540 Score = 26.8 bits (59), Expect = 8.0 Identities = 9/28 (32%), Positives = 13/28 (46%) Query: 229 ENVAVDLYNLTQSITSAHGLHAYEISNH 256 E+ AVDL +++ S H EI Sbjct: 483 EDKAVDLIVFKKAVLSTHHEKFDEIWER 510 >1r30_A Biotin synthase; SAM radical protein, TIM barrel, FES cluster, transferase; HET: SAM DTB; 3.40A {Escherichia coli} SCOP: c.1.28.1 Length = 369 Score = 26.7 bits (58), Expect = 9.1 Identities = 15/116 (12%), Positives = 36/116 (31%), Gaps = 10/116 (8%) Query: 28 CVKKCPYCDFNSHVRRYKVGQENF-IQSFLTEMQWMRQLTGPRSISSIFFGGGTPSLIEP 86 C + C YC + RYK G E + ++ R+ S Sbjct: 76 CPEDCKYCPQS---SRYKTGLEAERLMEVEQVLESARKAKAAGSTRFCMGAAWKN--PHE 130 Query: 87 QNIALILDGIAKNWTVSSNVEITIEANPSSVEVNNFQGYRKAGVNRISLGVQSLEE 142 +++ + + + + ++ + Q AG++ + + + E Sbjct: 131 RDMPYLEQMVQGVK----AMGLEACMTLGTLSESQAQRLANAGLDYYNHNLDTSPE 182 >3mwy_W Chromo domain-containing protein 1; SWI2/SNF2 ATPase, double chromodomains, hydrolase; HET: ATG; 3.70A {Saccharomyces cerevisiae} Length = 800 Score = 26.7 bits (58), Expect = 9.3 Identities = 14/91 (15%), Positives = 30/91 (32%), Gaps = 15/91 (16%) Query: 110 IEANPSSVEVNNFQGYRKAGVNRISLGVQSLEEQSLRF-------LGRNHNASEAIAAIH 162 + P ++ + ++ G+N ++ L + LG+ I+ + Sbjct: 225 LSVQPPFIKGGELRDFQLTGINWMA----FLWSKGDNGILADEMGLGKTVQTVAFISWLI 280 Query: 163 LARNIFPRMSFDLIYALPKQTMTQWEMELQR 193 AR +I P TM W ++ Sbjct: 281 FARRQNGPH---IIVV-PLSTMPAWLDTFEK 307 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 0.320 0.134 0.401 Gapped Lambda K H 0.267 0.0479 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,395,744 Number of extensions: 155235 Number of successful extensions: 432 Number of sequences better than 10.0: 1 Number of HSP's gapped: 427 Number of HSP's successfully gapped: 17 Length of query: 395 Length of database: 5,693,230 Length adjustment: 94 Effective length of query: 301 Effective length of database: 3,414,294 Effective search space: 1027702494 Effective search space used: 1027702494 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 58 (26.7 bits)