RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780751|ref|YP_003065164.1| ribonuclease E [Candidatus Liberibacter asiaticus str. psy62] (723 letters) >2bx2_L Ribonuclease E, RNAse E; RNA-binding, RNA turnover, RNA processing, hydrolase, endonuclease; 2.85A {Escherichia coli} PDB: 2c0b_L 2c4r_L 2vmk_A 2vrt_A 1slj_A 1smx_A 1sn8_A Length = 517 Score = 325 bits (835), Expect = 1e-89 Identities = 172/411 (41%), Positives = 255/411 (62%), Gaps = 3/411 (0%) Query: 159 DVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNKGAAVTTYLSLAGRYSVLMPNTSKGET 218 + I++V++ Q ++VQI KEERGNKGAA+TT++SLAG Y VLMPN + Sbjct: 86 PANYSAHGRPNIKDVLREGQEVIVQIDKEERGNKGAALTTFISLAGSYLVLMPNNPRA-G 144 Query: 219 ISRKITNPVDRKNLKEIARGLEVPAGMGVILRTAGASRTKIEIKRDFEYLMRLWDNVREL 278 + DR LKE LE+P GMG+I+RTAG ++ ++ D + ++ W+ +++ Sbjct: 145 GISRRIEGDDRTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLKHWEAIKKA 204 Query: 279 ALNSVAPHLVYEEGNLIKRAIRDLYCKDISEIIVSGEKGYREAKDFM-KLLMPSYARIVR 337 A + AP L+++E N+I RA RD +DI EI++ K A+ + L P ++ ++ Sbjct: 205 AESRPAPFLIHQESNVIVRAFRDYLRQDIGEILIDNPKVLELARQHIAALGRPDFSSKIK 264 Query: 338 QYEDPHPIFFRSGIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVNSGRSTREHCIED 397 Y P+F IE Q++S Q EV LPS G ++I+ TEAL +ID+NS R+TR IE+ Sbjct: 265 LYTGEIPLFSHYQIESQIESAFQREVRLPSGGSIVIDSTEALTAIDINSARATRGGDIEE 324 Query: 398 TALQTNLEAAEEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVG 457 TA TNLEAA+EIARQLRLRDL GLIV+DFIDM ++ R+VE +L+E++++DRAR+Q+ Sbjct: 325 TAFNTNLEAADEIARQLRLRDLGGLIVIDFIDMTPVRHQRAVENRLREAVRQDRARIQIS 384 Query: 458 AISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSILRSVEEYLLQYTAH 517 IS FGLLEMSRQR+ S+ ES+ VC C G G +R S++LSILR +EE L+ Sbjct: 385 HISRFGLLEMSRQRLSPSLGESSHHVCPRCSGTGTVRDNESLSLSILRLIEEEALKENTQ 444 Query: 518 NIIVHTHSDVVLYLLNQKRATIVEYEARF-GVSINVVIGIELADKLFYIEK 567 + + YLLN+KR+ + E R GV +V ++ +++ + Sbjct: 445 EVHAIVPVPIASYLLNEKRSAVNAIETRQDGVRCVIVPNDQMETPHYHVLR 495 Score = 131 bits (330), Expect = 6e-31 Identities = 48/111 (43%), Positives = 66/111 (59%), Gaps = 7/111 (6%) Query: 3 NKMLIDASHVEETRVVVLRDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYG 62 +MLI+A+ EE RV ++ R+ +LD ES +Q K NIY K+TR+EPSL+AAFVDYG Sbjct: 9 KRMLINATQQEELRVALVDGQRLYDLDIESPGHEQKKANIYKGKITRIEPSLEAAFVDYG 68 Query: 63 GNRHGFLPFLEIHPDYYQIPFSDR-----QALLKESN--IAQTDSEAVADD 106 RHGFLP EI +Y+ +S + +L+E I Q D E + Sbjct: 69 AERHGFLPLKEIAREYFPANYSAHGRPNIKDVLREGQEVIVQIDKEERGNK 119 >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 = 51.5 bits (123), Expect = 7e-07 Identities = 78/519 (15%), Positives = 151/519 (29%), Gaps = 175/519 (33%) Query: 19 VLRD-------NRVEELDFESEHKKQIKGNIYLAK-----VTRVEPSLQAAFVD-----Y 61 L++ E + E + + K + VEPS F Sbjct: 32 QLQEQFNKILPEPTEGFAADDEPTTPAE---LVGKFLGYVSSLVEPSKVGQFDQVLNLCL 88 Query: 62 GGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHGDVTIPNDHSL- 120 + +L +IH ++ + L+K + + A + ++ +L Sbjct: 89 TEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARI--MAKRPFDKKSNSALF 146 Query: 121 -----EEVAPIANFS-Q---ET--EE------------ESIISANNDVVSN-VEDVKGGS 156 +A F Q + EE +I + + +S + Sbjct: 147 RAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRT----- 201 Query: 157 PEDVPKKFKRQYCIQEVIKNRQILLVQIVKEERGNK----GAAVT----TYLSLAGRYSV 208 D K F + I E ++N +K ++ + LA Y V Sbjct: 202 TLDAEKVFTQGLNILEWLENP---------SNTPDKDYLLSIPISCPLIGVIQLA-HYVV 251 Query: 209 LMPNTSK--GETISRKITNPVDRKNLKEIARGLEVPAG--MGVILRTAGASRTKIEIKRD 264 T+K G T P E+ L+ G G++ A A E Sbjct: 252 ----TAKLLGFT-------P------GELRSYLKGATGHSQGLVTAVAIAETDSWE---S 291 Query: 265 FEYLMR------LWDNVREL---ALNSVAPHLVYE-----EGN----LIKRAIRDLYCKD 306 F +R + VR S+ P ++ + EG L +I +L + Sbjct: 292 FFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPML---SISNLTQEQ 348 Query: 307 ISEIIVSGEKGYREAKDFMKLLMPSYARIV-------RQY--EDPHPIFFRS--GIEVQL 355 + + + L P+ ++ + P P +S G+ + L Sbjct: 349 VQDYV----------NKTNSHL-PAGKQVEISLVNGAKNLVVSGP-P---QSLYGLNLTL 393 Query: 356 ------DSLHQTEVTLPSRGYVIINQTEALVSIDV--NSGRSTREHCIEDTA--LQTNLE 405 L Q+ + R N+ + + +S H + + + +L Sbjct: 394 RKAKAPSGLDQSRIPFSERKLKFSNR---FLPVASPFHS------HLLVPASDLINKDL- 443 Query: 406 AAEEI---ARQLR-----------LRDLAGLIVVDFIDM 430 + A+ ++ LR L+G I +D Sbjct: 444 VKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDC 482 Score = 43.4 bits (102), Expect = 2e-04 Identities = 53/215 (24%), Positives = 82/215 (38%), Gaps = 60/215 (27%) Query: 10 SHVEET------RVVVLRDNRVE-ELDFESEHKKQIKGNIYLAKV--TRVEPSLQAAFVD 60 +H ++T +V+ +N V + F E K+I+ N Y A + T V+ L+ + Sbjct: 1651 NHFKDTYGFSILDIVI--NNPVNLTIHFGGEKGKRIREN-YSAMIFETIVDGKLKTEKI- 1706 Query: 61 YGGNRHGFLPFLEIHPDYYQIPFSDRQALLKESNIAQ-----TDSEAVADDVTHGDVTIP 115 F EI+ F + LL + Q + A D + G IP Sbjct: 1707 ----------FKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKAAFEDLKSKG--LIP 1754 Query: 116 ND-----HSLEEVAPIANFSQETEEESIISANNDV---------VSNVEDVKGGS----- 156 D HSL E A +A+ + ES++ +V V+ D G S Sbjct: 1755 ADATFAGHSLGEYAALASLADVMSIESLV----EVVFYRGMTMQVAVPRDELGRSNYGMI 1810 Query: 157 ---PEDVPKKFKR---QYCIQEVIKNRQILLVQIV 185 P V F + QY ++ V K R LV+IV Sbjct: 1811 AINPGRVAASFSQEALQYVVERVGK-RTGWLVEIV 1844 Score = 39.5 bits (92), Expect = 0.002 Identities = 47/274 (17%), Positives = 89/274 (32%), Gaps = 101/274 (36%) Query: 21 RDNRVEELDFESEHKKQIKGNIYLAKVTRVEPSL---QAAFVD-------YGGNRHGFLP 70 + E++ ++ + N +L +VE SL V YG N Sbjct: 342 SNLTQEQVQ---DYVNKT--NSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLT---- 392 Query: 71 FL-EI----HPDYYQIPFSDRQALLKESNIAQTDSEAVADDVTHG--DVTIPNDHS--LE 121 L + D +IPFS+R+ ++ V P HS L Sbjct: 393 -LRKAKAPSGLDQSRIPFSERKL-----------------KFSNRFLPVASPF-HSHLLV 433 Query: 122 EVAPIANFSQETEEESI-ISANNDVVSNVEDVKGGSPEDVPKKFKRQYCIQEVIKNRQIL 180 + + +++ + ++ +A D+ V D G D ++ + + I Sbjct: 434 PASDLI--NKDLVKNNVSFNA-KDIQIPVYDTFDG--SD----------LRVLSGS--IS 476 Query: 181 --LVQIVKEERGNKGAAVT---TYLSLAGRYSVLMPNTSKGETISRKITNPVDRKNLKEI 235 +V + T++ G P + G + +T+ +N K+ Sbjct: 477 ERIVDCIIRLPVKWETTTQFKATHILDFG------PGGASG--LGV-LTH----RN-KD- 521 Query: 236 ARGLEVPAGMG--VILRTAGASRTKIEIKRDFEY 267 G G VI+ AG ++I D +Y Sbjct: 522 --------GTGVRVIV--AGT----LDINPDDDY 541 Score = 38.8 bits (90), Expect = 0.005 Identities = 65/331 (19%), Positives = 124/331 (37%), Gaps = 108/331 (32%) Query: 244 GMGVIL-RTAGAS-----RTKIEIKRDFEYLMRLWDNVRELALNS---VAPHLVYEEGNL 294 GMG+ L +T+ A+ R K + + ++ ++ +N+ + H E+G Sbjct: 1630 GMGMDLYKTSKAAQDVWNRADNHFKDTYGF------SILDIVINNPVNLTIHFGGEKG-- 1681 Query: 295 IKRAIRDLYCKDISEIIVSG----EKGYREAKDFMKLLMPSYARIVRQYEDPHPIFFRS- 349 KR IR+ Y I E IV G EK ++E + SY FRS Sbjct: 1682 -KR-IRENYSAMIFETIVDGKLKTEKIFKEINEHST----SYT-------------FRSE 1722 Query: 350 -GIEVQLDSLHQTEVTLPSRGYVIINQTEALVSIDVN-SGRSTREHCIEDTALQTNLEAA 407 G+ + Q +TL + +++ L+ D +G S E+ A Sbjct: 1723 KGL-LSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYA-----------AL 1770 Query: 408 EEIARQLRLRDLAGLIVVDFIDMEEKKNNRSVEKKLKESLKKDRARVQVGAISNFGLLEM 467 +A + + L ++ + M+ ++ +D ++G SN+G++ + Sbjct: 1771 ASLADVMSIESLVEVVFYRGMTMQ-------------VAVPRD----ELGR-SNYGMIAI 1812 Query: 468 SRQRIRSS--------VLESTTK-------VCTYCKGAGYIRSQSSVALSILRSVEEYLL 512 + R+ +S V+E K + Y + +Q VA LR+++ Sbjct: 1813 NPGRVAASFSQEALQYVVERVGKRTGWLVEIVNY-----NVENQQYVAAGDLRALD---- 1863 Query: 513 QYTAHNIIVHTHSDVVLYLLNQKRATIVEYE 543 T N VL + ++ I+E + Sbjct: 1864 --TVTN---------VLNFIKLQKIDIIELQ 1883 Score = 38.0 bits (88), Expect = 0.007 Identities = 32/234 (13%), Positives = 70/234 (29%), Gaps = 89/234 (38%) Query: 506 SVEEYLLQYTAHNIIVH--------THSDVVLYLLNQKRATIVEYEARF--GVSINVVI- 554 + E + ++ + + V+ L E+E + G I+ + Sbjct: 56 TPAELVGKFLGY--VSSLVEPSKVGQFDQVLNLCLT-------EFENCYLEGNDIHALAA 106 Query: 555 ------GIELADKLFYIEKGSPVQALVNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPK 608 L I+ + + A + D ++ S AL Sbjct: 107 KLLQENDTTLVKTKELIK--NYITARIMAKRP--FDKKSNS------------ALF---- 146 Query: 609 SESLEDIQDNIVS------------EESTGVIRKRRRRRRRRRPATDHHD--AGVVSD-V 653 ++ + +V+ EE +R D + +V D + Sbjct: 147 -RAVGEGNAQLVAIFGGQGNTDDYFEE----LR-------------DLYQTYHVLVGDLI 188 Query: 654 SSIQNVI-------DDSFDMYMEPSDITNHNLLENGAHGFTENYDVSIPPVSTP 700 + D+ ++ + +I LEN ++ ++Y +SI P+S P Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQGLNI--LEWLENPSNTPDKDYLLSI-PISCP 239 >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 = 31.5 bits (70), Expect = 0.63 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 22/50 (44%) Query: 566 EKGSPVQAL--VNTGHKVGSDSQAPSYDKNIECVWQDEALLPIPKSESLE 613 EK QAL + K+ +D AP+ L I K+ ++E Sbjct: 18 EK----QALKKLQASLKLYADDSAPA--------------LAI-KA-TME 47 Score = 31.5 bits (70), Expect = 0.75 Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 7/24 (29%) Query: 432 EKKNNRSVEKKLKESLK---KDRA 452 EK+ ++ KKL+ SLK D A Sbjct: 18 EKQ---AL-KKLQASLKLYADDSA 37 Score = 30.0 bits (66), Expect = 2.2 Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 36/65 (55%) Query: 444 KESLKKDRARVQVGAISNFGLLEMSRQRIRSSVLESTTKVCTYCKGAGYIRSQSSVALSI 503 K++LKK L+++ K+ Y S+ AL+I Sbjct: 19 KQALKK---------------------------LQASLKL--YA-------DDSAPALAI 42 Query: 504 LRSVE 508 ++E Sbjct: 43 KATME 47 Score = 29.6 bits (65), Expect = 2.9 Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 10/31 (32%) Query: 85 DRQALLKESNIAQTDSEAVADDVTHGDVTIP 115 ++QAL K Q + ADD + P Sbjct: 18 EKQALKK----LQASLKLYADD------SAP 38 >3cdi_A Polynucleotide phosphorylase; mRNA turnover, RNAse, RNA degradation, kinase, transferase; 2.60A {Escherichia coli} PDB: 1sro_A Length = 723 Score = 30.6 bits (69), Expect = 1.3 Identities = 24/90 (26%), Positives = 34/90 (37%), Gaps = 28/90 (31%) Query: 23 NRVEELDFESEHKKQIKGNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEIHPDYYQIP 82 R+EE+ E E G +Y KVTR+ VD+G F+ I Sbjct: 616 RRIEEITAEIE-----VGRVYTGKVTRI--------VDFGA-------FVAIGG------ 649 Query: 83 FSDRQALLKESNIAQTDSEAVADDVTHGDV 112 ++ L+ S IA E V D + G Sbjct: 650 --GKEGLVHISQIADKRVEKVTDYLQMGQE 677 >1iru_N 20S proteasome; cell cycle, immune response, proteolysis, ubiquitin, hydrolase; 2.75A {Bos taurus} SCOP: d.153.1.4 Length = 219 Score = 28.9 bits (64), Expect = 4.4 Identities = 14/62 (22%), Positives = 23/62 (37%), Gaps = 6/62 (9%) Query: 285 PHLVYEEG-NLIKRAIRDLYCKDIS-----EIIVSGEKGYREAKDFMKLLMPSYARIVRQ 338 P L E +L++R +R LY +D + EKG A ++ Sbjct: 158 PVLSQTEARDLVERCMRVLYYRDARSYNRFQTATVTEKGVEIEGPLSTETNWDIAHMISG 217 Query: 339 YE 340 +E Sbjct: 218 FE 219 >2epj_A Glutamate-1-semialdehyde 2,1-aminomutase; PLP enzyme, GSA, structural genomics, NPPSFA; HET: PMP; 1.70A {Aeropyrum pernix K1} PDB: 2zsl_A* 2zsm_A* Length = 434 Score = 28.8 bits (63), Expect = 5.0 Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 6/45 (13%) Query: 309 EIIVSGEKG---YREAKDFMKLLMPSYARIVRQYEDPHPIFFRSG 350 +++ SGEK + K+ + S VR P+P + + G Sbjct: 4 DVLASGEKSRMLFERTKELFPGGVNSP---VRAAVKPYPFYVKRG 45 >2pe4_A Hyaluronidase-1; hyaluronan, EGF-like domain, alternative splicing, hydrolase; HET: NAG BMA MAN; 2.00A {Homo sapiens} Length = 424 Score = 28.2 bits (63), Expect = 6.9 Identities = 8/29 (27%), Positives = 15/29 (51%), Gaps = 1/29 (3%) Query: 400 LQTNLE-AAEEIARQLRLRDLAGLIVVDF 427 L +L ++I + D +GL V+D+ Sbjct: 83 LIAHLARTFQDILAAIPAPDFSGLAVIDW 111 >1knv_A BSE634I restriction endonuclease; APO-enzyme, hydrolase; 2.17A {Geobacillus stearothermophilus} SCOP: c.52.1.7 Length = 293 Score = 28.0 bits (62), Expect = 7.2 Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 3/45 (6%) Query: 262 KRDFEYLMRLWDNV---RELALNSVAPHLVYEEGNLIKRAIRDLY 303 K +F+Y + V + AL + A H + + +RA+ D++ Sbjct: 231 KAEFKYYGASSEPVSKADDDALQTAATHTIVNVNSTPERAVDDIF 275 >1e3p_A Guanosine pentaphosphate synthetase; polyribonucleotide transferase, ATP-GTP diphosphotransferase RNA processing, RNA degradation; 2.5A {Streptomyces antibioticus} SCOP: a.4.9.1 b.40.4.5 d.14.1.4 d.14.1.4 d.52.3.1 d.101.1.1 d.101.1.1 PDB: 1e3h_A Length = 757 Score = 27.8 bits (62), Expect = 7.6 Identities = 9/35 (25%), Positives = 12/35 (34%), Gaps = 2/35 (5%) Query: 40 GNIYLAKVTRVEPSLQAAFVDYGGNRHGFLPFLEI 74 G L V + AFV + G L +I Sbjct: 668 GERILGSVVKTTTF--GAFVSLLPGKDGLLHISQI 700 >1d6t_A Ribonuclease P, RNAse P protein; endonuclease, subunit; NMR {Staphylococcus aureus} SCOP: d.14.1.2 Length = 117 Score = 27.8 bits (62), Expect = 9.3 Identities = 14/63 (22%), Positives = 27/63 (42%), Gaps = 7/63 (11%) Query: 216 GETISRKITNPVDRKNLKEIARGLEVPAGMG-------VILRTAGASRTKIEIKRDFEYL 268 G ++S+K+ N V R +K R VI R T ++I+ E++ Sbjct: 46 GISVSKKLGNAVLRNKIKRAIRENFKVHKSHILAKDIIVIARQPAKDMTTLQIQNSLEHV 105 Query: 269 MRL 271 +++ Sbjct: 106 LKI 108 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 0.316 0.132 0.369 Gapped Lambda K H 0.267 0.0664 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 6,130,040 Number of extensions: 295659 Number of successful extensions: 1256 Number of sequences better than 10.0: 1 Number of HSP's gapped: 1235 Number of HSP's successfully gapped: 32 Length of query: 723 Length of database: 5,693,230 Length adjustment: 99 Effective length of query: 624 Effective length of database: 3,293,074 Effective search space: 2054878176 Effective search space used: 2054878176 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 (21.6 bits) S2: 60 (27.0 bits)