RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780837|ref|YP_003065250.1| putative restriction endonuclease S subunit [Candidatus Liberibacter asiaticus str. psy62] (426 letters) >1yf2_A Type I restriction-modification enzyme, S subunit; structural genomics, PSI, protein structure initiative; 2.40A {Methanocaldococcus jannaschii DSM2661} SCOP: d.287.1.2 d.287.1.2 Length = 425 Score = 102 bits (254), Expect = 2e-22 Identities = 70/438 (15%), Positives = 157/438 (35%), Gaps = 40/438 (9%) Query: 7 YPQYKDSGVQWIGAIPKHWKVVPIKR-FTKLNTGRTSESGK-------DIIYIGLEDVES 58 +K + IG IP+ W++V +K K+ G T ++ I ++ +ED+ + Sbjct: 5 EENFKKT---EIGEIPEDWEIVELKDVCKKIKAGGTPKTSVEEYYKNGTIPFVKIEDITN 61 Query: 59 GTGKYLPKDG---NSRQSDTSTVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQ 115 KYL + S I K +L+ G AI ++ Sbjct: 62 S-NKYLTNTKIKITEEGLNNSNAWIVPKNSVLFAMYGSIGETAINKIEVATNQAILGIIP 120 Query: 116 PKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLIREKII 175 ++L + + + T + + + + + +P+PPL EQ I + + Sbjct: 121 KDNILESEFL-YYILAKNKNYYSKLGMQTTQKNLNAQIVKSFKIPLPPLEEQKQIAKILT 179 Query: 176 AETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVK 235 I+ + + L+ K+ L+ ++TKG+ K +G +P+ WEV Sbjct: 180 KIDEGIEIIEKSINK----LERIKKGLMHKLLTKGIGHSRFKKSE----IGEIPEDWEVF 231 Query: 236 PFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESYETYQIVDPGEIVFRF 295 + +S N I L+ + K + + V + Sbjct: 232 EIKDIFEVKTGTTPSTKKSEYWENGEINWITPLDLSRLNEKIYIGSSERKVTKIALEKCN 291 Query: 296 IDLQNDKRSLRSAQVMERGIITSAYMAVKPHG-----------IDSTYLAWLMRSYDLCK 344 ++L + S + + + G +++ + A+ ++ Sbjct: 292 LNLIPKGSIIISTRAPVGYVAVLTVESTFNQGCKGLFQKNNDSVNTEFYAYYLKFKKNLL 351 Query: 345 VFYAMGSGLRQSLKFEDVKRLPVLVPPIKEQFDITNVINVETARIDVLVEKIEQSIVLLK 404 + GS + L ++ + +PP++EQ I +++ +D +E +Q L+ Sbjct: 352 ENLSGGST-FKELSKSMLENFKIPLPPLEEQKQIAKILS----SVDKSIELKKQKKEKLQ 406 Query: 405 ERRSSFIAAAVTGQIDLR 422 + + +TG++ ++ Sbjct: 407 RMKKKIMELLLTGKVRVK 424 Score = 64.8 bits (156), Expect = 4e-11 Identities = 40/218 (18%), Positives = 76/218 (34%), Gaps = 15/218 (6%) Query: 2 KHYKAYPQYKDSGVQWIGAIPKHWKVVPIKRFTKLNTGRTSESGK-------DIIYIGLE 54 K + IG IP+ W+V IK ++ TG T + K +I +I Sbjct: 205 KLLTKGIGHSRFKKSEIGEIPEDWEVFEIKDIFEVKTGTTPSTKKSEYWENGEINWITPL 264 Query: 55 DVESGTGKYLPKDGNSRQSDT----STVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQ 110 D+ K + + +++ KG I+ P A++ Sbjct: 265 DLSRLNEKIYIGSSERKVTKIALEKCNLNLIPKGSIIISTRAPVGYVAVLTVESTFNQGC 324 Query: 111 FLVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADWKGIGNIPMPIPPLAEQVLI 170 + Q + +E + G+T + N +P+PPL EQ Sbjct: 325 KGLFQKNNDSVNTEFYAYYLKFKKNLLENLSGGSTFKELSKSMLENFKIPLPPLEEQ--- 381 Query: 171 REKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVT 208 ++I +D I + + E L+ K+ ++ ++T Sbjct: 382 -KQIAKILSSVDKSIELKKQKKEKLQRMKKKIMELLLT 418 >1ydx_A Type I restriction enzyme specificity protein Mg438; type-I HSDS, DNA binding protein; 2.30A {Mycoplasma genitalium} SCOP: d.287.1.2 d.287.1.2 Length = 406 Score = 67.8 bits (164), Expect = 5e-12 Identities = 45/400 (11%), Positives = 99/400 (24%), Gaps = 39/400 (9%) Query: 25 WKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTSTVSIFAKG 84 W I L G E ++ + GKY +G + S + K Sbjct: 36 WTKRTIDSLFDLKKGEMLEK----------ELITPEGKYEYFNGGVKNSGRTDKFNTFKN 85 Query: 85 QILYGKLGPYLRKAIIAD--FDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQRIEAICE 142 I G + F G + +L P ++ + L S +RIEA+ Sbjct: 86 TISVIVGGSCGYVRLADKNFFCGQSNCTLNLLDPLELDLKFAYYALKSQQ--ERIEALAF 143 Query: 143 GATMSHADWKGIGNIPMPIPPLAEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQAL 202 G T+ + + + +P + + I D + IE+ ++ + Sbjct: 144 GTTIQNIRISDLKELEIPFTSNKNE---QHAIANTLSVFDERLENLASLIEINRKLRDEY 200 Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIESNILSLSYG 262 + + K + + + K K Sbjct: 201 AHKLFSLDEAFLSHWKLEAL------QSQMHEITLGEIFNFKSGKYLKS--------EER 246 Query: 263 NIIQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMA 322 K G+ + + I S + Sbjct: 247 LEEGKFPYYGAGIDNTGFVAEPNTEKDTISIISNGYSLGNIRYHEIPWFNGT--GSIALE 304 Query: 323 VKPHGIDSTYLAWLMRSYDLCKVFYAMGSGLRQSLKFEDVKRLPV-LVPPIKEQFDITNV 381 + I + ++ L + + V V + Q + Sbjct: 305 PMNNEIYVPFFYCALKYLQKDIKERMKSDD-SPFLSLKLAGEIKVPYVKSFQLQRKAGKI 363 Query: 382 INVETARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDL 421 + +D +++ ++ + L R + + + Sbjct: 364 VF----LLDQKLDQYKKELSSLTVIRDTLLKKLFPDMTER 399 Score = 50.4 bits (119), Expect = 8e-07 Identities = 21/187 (11%), Positives = 50/187 (26%), Gaps = 15/187 (8%) Query: 17 WIGAIPKHWKVVPIKRFTKLNTGRTSESGKDIIYIGLEDVESGTGKYLPKDGNSRQSDTS 76 + A+ + + +G+ +S + + K+ + Sbjct: 216 KLEALQSQMHEITLGEIFNFKSGKYLKSEERLEEG----------KFPYYGAGIDNTGFV 265 Query: 77 TVSIFAKGQILYGKLGPYLRKAIIADFDGICSTQFLVLQPKDVLPELLQGWLLSIDVTQR 136 K I G L + T + L+P + + + + + Sbjct: 266 AEPNTEKDTISIISNGYSLGNIRYHEIPWFNGTGSIALEPMNNEIYVPFFYCALKYLQKD 325 Query: 137 IEAICEGATMSHADWKGIGNIPMP-IPPLAEQVLIREKIIAETVRIDTLITERIRFIELL 195 I+ + K G I +P + Q K +D + + + + L Sbjct: 326 IKERMKSDDSPFLSLKLAGEIKVPYVKSFQLQ----RKAGKIVFLLDQKLDQYKKELSSL 381 Query: 196 KEKKQAL 202 + L Sbjct: 382 TVIRDTL 388 >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 = 50.3 bits (120), Expect = 7e-07 Identities = 70/439 (15%), Positives = 144/439 (32%), Gaps = 174/439 (39%) Query: 65 PKDGNSRQSD-TSTVSIFAK--GQILY----GKLGPYLR--KAIIADFDGICSTQFLVLQ 115 P +G + + T+ + K G + K+G + + + +F+ +L + Sbjct: 44 PTEGFAADDEPTTPAELVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFE----NCYL--E 97 Query: 116 PKDV------LP-----------ELLQGWLLSIDVTQR----------IEAICEGATMSH 148 D+ L EL++ ++ + + +R A+ EG Sbjct: 98 GNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLV 157 Query: 149 ADWKGIGNIPMPIPPLAEQVL--IREKIIAETVR--IDTLITERI--RFIELLKEKKQAL 202 A + G GN + +R+ + +T + LI + EL++ A Sbjct: 158 AIFGGQGNT--------DDYFEELRD--LYQTYHVLVGDLI-KFSAETLSELIRTTLDA- 205 Query: 203 VSYIVTKGLNPDVKMKDSGIEWVGL-----VPDHWEVKPFFALVT-ELNRKNTKLIESNI 256 + T+GL ++ +EW L PD K + + LI + Sbjct: 206 -EKVFTQGL--NI------LEW--LENPSNTPD----KDYLLSIPISC-----PLI--GV 243 Query: 257 LSL-SYGNIIQKLET-RNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSA----QV 310 + L Y ++ T + +G PGE R L+ A Q Sbjct: 244 IQLAHY--VV----TAKLLGF-----------TPGE--LR--------SYLKGATGHSQ- 275 Query: 311 MERGIITSAYMAVKPHGIDSTYLAWLMRS-YDLCK-----VFYAMGSGLRQSLKFEDVKR 364 G++T+ +A DS W S + + +F+ G+R + Sbjct: 276 ---GLVTAVAIAET----DS----W--ESFFVSVRKAITVLFF---IGVRCYEAY----- 314 Query: 365 LPVL-VPPIKEQFDITN-------VINVETARIDVLVEKIEQ-----------SIVLLKE 405 P +PP + + N ++++ + + + + + I L+ Sbjct: 315 -PNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNG 373 Query: 406 RRSSFIAAAVTG-QIDLRG 423 + + + V+G L G Sbjct: 374 AK-NLV---VSGPPQSLYG 388 Score = 47.2 bits (112), Expect = 7e-06 Identities = 83/461 (18%), Positives = 125/461 (27%), Gaps = 214/461 (46%) Query: 60 TGKYLPKDGNS------RQSDTSTVSIFAKGQILYGKLGPY---LR------KAIIADFD 104 + K NS + + V+IF GQ G Y LR ++ D Sbjct: 133 AKRPFDKKSNSALFRAVGEGNAQLVAIFG-GQ---GNTDDYFEELRDLYQTYHVLVGDLI 188 Query: 105 GICSTQF--LVLQPKDVLPELLQGWLLSIDVTQRIEAICEGATMSHADW-KGIGNIPMPI 161 + L+ D QG +++ + W + P Sbjct: 189 KFSAETLSELIRTTLDAEKVFTQG----LNILE---------------WLEN----PSNT 225 Query: 162 PPLAEQVLIREKIIAETVRIDTLITERIRF--IELLKEKKQALVSYIVT-K--GLNPDVK 216 P D L++ I I ++ Q L Y+VT K G P + Sbjct: 226 PD-----------------KDYLLSIPISCPLIGVI----Q-LAHYVVTAKLLGFTPG-E 262 Query: 217 MKDSGIEWV-----GLVP-------DHWEVKPFFALVTELNRKNTKLIESNILSLSYGNI 264 ++ ++ GLV D WE FF V RK + L + Sbjct: 263 LRSY-LKGATGHSQGLVTAVAIAETDSWE--SFFVSV----RKAITV-------LFF--- 305 Query: 265 IQKLETRNMGLKPESYETYQIVDPGEIVFRFIDLQNDKRSLRSAQV---MERGIITSAYM 321 +G+ YE Y P SL + + +E + M Sbjct: 306 --------IGV--RCYEAY----P-------------NTSLPPSILEDSLENNEGVPSPM 338 Query: 322 ---------AVKPHGIDST----------YLAWLMRS-------------YDLCKVFYAM 349 V+ + ++ T ++ L+ Y L Sbjct: 339 LSISNLTQEQVQDY-VNKTNSHLPAGKQVEIS-LVNGAKNLVVSGPPQSLYGLNLTLRKA 396 Query: 350 G--SGLRQS--------LKFEDVKR-LPVLVP---P--------IKEQFDITNV-INVET 386 SGL QS LKF R LPV P I + NV N + Sbjct: 397 KAPSGLDQSRIPFSERKLKF--SNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKD 454 Query: 387 ARIDVLVEKIEQSIVLLKERRSSFIAAAVTGQIDLR--GES 425 +I V +F G DLR S Sbjct: 455 IQIPVY---------------DTF-----DGS-DLRVLSGS 474 Score = 38.4 bits (89), Expect = 0.003 Identities = 50/277 (18%), Positives = 76/277 (27%), Gaps = 127/277 (45%) Query: 17 WIG-----AIPKHWKVVPIKRFTKLNTGRTS----------ESGKD-------IIYIGLE 54 +IG A P TS E+ + I + E Sbjct: 305 FIGVRCYEAYP-----------------NTSLPPSILEDSLENNEGVPSPMLSISNLTQE 347 Query: 55 DVES---GTGKYLPKDG-------NSRQSDTSTVSIFAKG--QILYGKLGPYLRKAIIAD 102 V+ T +LP N ++ VS G Q LYG L LRK A Sbjct: 348 QVQDYVNKTNSHLPAGKQVEISLVNGAKN--LVVS----GPPQSLYG-LNLTLRK-AKAP 399 Query: 103 FDGI-------------CSTQFLVLQPKDVLP---ELLQGWLLSIDVTQRIEA--ICEGA 144 G+ S +FL P P LL + I + Sbjct: 400 -SGLDQSRIPFSERKLKFSNRFL---PVAS-PFHSHLLV------PASDLINKDLVKNNV 448 Query: 145 TMSHADWKGIGNIPMPIPPLAEQVL-------IR---EKIIAETVRIDTLIT-ERIRFIE 193 + + D + IP V +R I V I +++ Sbjct: 449 SFNAKDIQ----IP---------VYDTFDGSDLRVLSGSISERIVD---CIIRLPVKWET 492 Query: 194 LLKEKKQALVSYIV------TKGLNPDV-KMKD-SGI 222 + K ++I+ GL + KD +G+ Sbjct: 493 TTQFK----ATHILDFGPGGASGLGVLTHRNKDGTGV 525 Score = 35.3 bits (81), Expect = 0.029 Identities = 46/275 (16%), Positives = 87/275 (31%), Gaps = 113/275 (41%) Query: 257 LSLSYGNI-------------IQKL-ETRNMGLKPESYETYQIVD----PGEIVFRFI-- 296 L+LS+G++ +L E N L PE E + D P E+V +F+ Sbjct: 9 LTLSHGSLEHVLLVPTASFFIASQLQEQFNKIL-PEPTEGFAADDEPTTPAELVGKFLGY 67 Query: 297 --DLQNDKRSLRSAQVMERGI--ITSAYM--------AVKPHGIDSTYLAWLMRSYDLCK 344 L + + QV+ + + Y+ A K + T L ++ +L K Sbjct: 68 VSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLV---KTKELIK 124 Query: 345 VFY----AMG--------SGLRQSLK-------------------FEDVKRL-----PVL 368 + S L +++ FE+++ L ++ Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184 Query: 369 VPPIKEQFDITNVINVETARIDVLVEKI-EQSIVLLK-----ERR--SSFIAAA------ 414 IK ++ E R + EK+ Q + +L+ ++ + Sbjct: 185 GDLIKF---SAETLS-ELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPL 240 Query: 415 ----------VTGQI------DLR-------GESQ 426 VT ++ +LR G SQ Sbjct: 241 IGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQ 275 >3opc_A Uncharacterized protein; structural genomics, PSI-2, protein structure initiative, MI center for structural genomics, MCSG, chaperone; HET: MSE; 2.09A {Bordetella pertussis} Length = 154 Score = 30.6 bits (68), Expect = 0.66 Identities = 17/117 (14%), Positives = 36/117 (30%), Gaps = 5/117 (4%) Query: 165 AEQVLIREKIIAETVRIDTLITERIRFIELLKEKKQALVSYIVTKGLNPDVKMKDSGIEW 224 AE + ++ E+ + + + + L + + + GL D Sbjct: 29 AETEALMDRRAHES--LQAAVQRKETLADDLAQLGAERDALLSGAGLASGPAGTDXXXXX 86 Query: 225 VGLVPDHW-EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETRNMGLKPESY 280 + W ++ A E N++N LI N+ + L +Y Sbjct: 87 HPELGPLWQALQANAAQAREHNQRNGTLIAVNLRHTQ--ESLDALRQAAGTGAAATY 141 >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 = 30.0 bits (66), Expect = 0.93 Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 30/58 (51%) Query: 198 KKQALVSYIVTKGLNPDVKM--KDSGIEWVGLVPDHWEVKPFFALVTELNRKNTKLIE 253 +KQAL K L +K+ DS P A+ K T +E Sbjct: 18 EKQAL------KKLQASLKLYADDSA--------------PALAI------KAT--ME 47 >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 = 29.4 bits (65), Expect = 1.6 Identities = 26/112 (23%), Positives = 47/112 (41%), Gaps = 25/112 (22%) Query: 233 EVKPFFALVTELNRKNTKLIESNILSLSYGNIIQKLETR-NMGLK-PE--SYETYQIVDP 288 EV+ ++ T L K ++ N +Y + +++ R N+ L PE Y+ + + P Sbjct: 753 EVRKAVSIETALEHK---VVNGNSADAAYAQV--EIQPRANIQLDFPELKPYKQVKQIAP 807 Query: 289 GEIVFRFIDLQNDKRSLRSAQVMERGIITSAYMAVKPHGIDSTYLAWLMRSY 340 E+ +DL ER I+ + + V P G S W M ++ Sbjct: 808 AELE-GLLDL-------------ERVIVVTGFAEVGPWG--SARTRWEMEAF 843 >2r5t_A Serine/threonine-protein kinase SGK1; AGC protein kinase, apoptosis, ATP-binding, cytoplasm, endoplasmic reticulum, nucleotide-binding, nucleus; HET: ANP; 1.90A {Homo sapiens} PDB: 3hdm_A* 3hdn_A* Length = 373 Score = 27.0 bits (59), Expect = 7.9 Identities = 28/119 (23%), Positives = 45/119 (37%), Gaps = 17/119 (14%) Query: 59 GTGKYLPKDGNSRQSDTSTVSIFAKGQILY----GKLGPYLRKAIIADFDGICSTQFLVL 114 GT +YL + +Q TV + G +LY G P+ + +D I + + Sbjct: 201 GTPEYLAPEVLHKQPYDRTVDWWCLGAVLYEMLYGLP-PFYSRNTAEMYDNILNKPLQL- 258 Query: 115 QPKDVLPEL--LQGWLLSIDVTQRIEAICEGAT-MSHA-----DWKGIGN--IPMPIPP 163 ++ L LL D T+R+ A + SH +W + N I P P Sbjct: 259 -KPNITNSARHLLEGLLQKDRTKRLGAKDDFMEIKSHVFFSLINWDDLINKKITPPFNP 316 >2c30_A Serine/threonine-protein kinase PAK 6; STE20-like, CRIB domain, ATP-binding, transferase, nucleotide-binding, phosphorylation, polymorphism; HET: SEP; 1.6A {Homo sapiens} PDB: 2f57_A* 2j0i_A* 2cdz_A* 2q0n_A* 2bva_A* Length = 321 Score = 26.9 bits (59), Expect = 8.3 Identities = 16/88 (18%), Positives = 35/88 (39%), Gaps = 8/88 (9%) Query: 59 GTGKYLPKDGNSRQSDTSTVSIFAKGQILY----GKLGPYLRKAIIADFDGICSTQFLVL 114 GT ++ + SR + V I++ G ++ G+ PY + + + + L Sbjct: 203 GTPYWMAPEVISRSLYATEVDIWSLGIMVIEMVDGEP-PYFSDSPVQAMKRLRDSPPPKL 261 Query: 115 QPKDVLPELLQ---GWLLSIDVTQRIEA 139 + + +L+ +L D +R A Sbjct: 262 KNSHKVSPVLRDFLERMLVRDPQERATA 289 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 0.319 0.138 0.400 Gapped Lambda K H 0.267 0.0597 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 3,755,610 Number of extensions: 179229 Number of successful extensions: 427 Number of sequences better than 10.0: 1 Number of HSP's gapped: 419 Number of HSP's successfully gapped: 20 Length of query: 426 Length of database: 5,693,230 Length adjustment: 95 Effective length of query: 331 Effective length of database: 3,390,050 Effective search space: 1122106550 Effective search space used: 1122106550 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 (26.4 bits)