RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780760|ref|YP_003065173.1| hypothetical protein CLIBASIA_03235 [Candidatus Liberibacter asiaticus str. psy62] (330 letters) >2eqa_A Hypothetical protein ST1526; YRDC/RIBB fold, YRDC domain, SUA5 domain, structural genomics, NPPSFA; HET: AMP; 1.80A {Sulfolobus tokodaii} Length = 352 Score = 188 bits (479), Expect = 1e-48 Identities = 82/328 (25%), Positives = 136/328 (41%), Gaps = 15/328 (4%) Query: 8 DSNALRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAMNPLICHVSDI 67 + + ++ A + + G +A PTETVYGL ++ + A ++++ K RP NPLI H++D Sbjct: 13 EIDKIKIAADVIRNGGTVAFPTETVYGLGANAFDGNACLKIFQAKNRPVDNPLIVHIADF 72 Query: 68 SMVKKHASVDPLSLHLAKLFWPGPLTLVLDLLSTTDIHPLSTANLKTACFRVPCGFTKKL 127 + + + A P + + + ++ A +L Sbjct: 73 NQLFEVAKDIPDKVLEIAQIVWPGPLTFVLKKTERVPKEVTAGLDTVAVRMPAHPIALQL 132 Query: 128 IETYGHPLAIPSANRSGQISITNVKHILSSSICKEIPLIIDGGISKIGLESTIVNVQCEK 187 I G P+A PSAN + + S T + ++ + + +IIDGG + G+ESTI+NV E Sbjct: 133 IRESGVPIAAPSANLATRPSPTKAEDVI-VDLNGRVDVIIDGGHTFFGVESTIINVTVEP 191 Query: 188 KVRILRPGGLEIETLKRAI----SVELEYCVDETSTPQSPGMLKSHYAPRSQVRLRAIHV 243 +LRPG IE LK+ E E +PGM HYAP +++ L Sbjct: 192 P-VLLRPGPFTIEELKKLFGEIVIPEFAQGKKEAEIALAPGMKYKHYAPNTRLLLVENRN 250 Query: 244 NPREALIRFGN---------VPIKNIENAIISLNLSKTGKLKEAAFNLFNYMKIADDSGA 294 ++ + + + + L L E A NLF+ + D Sbjct: 251 IFKDVVSLLSKKYKVALLIPKELSKEFEGLQQIILGSDENLYEVARNLFDSFRELDKLNV 310 Query: 295 SSIAFSSIPNHGLGIAINNRLERAAAPR 322 P G+G AI NR +A+ Sbjct: 311 DLGIMIGFPERGIGFAIMNRARKASGFS 338 >3l7v_A Putative uncharacterized protein SMU.1377C; transcription; 2.26A {Streptococcus mutans} Length = 295 Score = 155 bits (393), Expect = 1e-38 Identities = 42/244 (17%), Positives = 81/244 (33%), Gaps = 48/244 (19%) Query: 8 DSNALRKACEFLDA-GLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAMNPLICHVSD 66 D N ++ E + G I PT+ Y + + + R +E KKR P + Sbjct: 42 DGNLSQEGFEIVKGEGGVIVCPTKVGYIIMTS--DKKGLERKFEAKKRNRNKPGVVLCGS 99 Query: 67 ISMVKKHASVDPLSLHLAKLFWPGPLTLVLDLLSTTDIHP---------------LSTAN 111 + ++ A + P + W + L L + + + + Sbjct: 100 MEELRALAQLTPEIDAFYQKHWDEDILLGCILPWKAEAYEKLKAYGDGREELMTDIRGTS 159 Query: 112 LKTACFRVP-CGFTKKLIETYGHPLAIPSANRSGQISITNVKHILSSSICKEIPLIIDGG 170 F V K++ E G + SAN SG+ + V+ I I + L+I+ Sbjct: 160 CFVIKFGVAGEQIAKEMWEKEGRMVYASSANPSGKGNRGKVEGIG-ERIESMVDLVIEAD 218 Query: 171 --------------ISKIGLESTIVNV-------------QCEKKVRILRPGGLEIETLK 203 + G+ ++V+ E ++R GL+I+ + Sbjct: 219 DYVASIQPDKTIETRYEQGVMVSMVDKDGKLIPQQGADSRSVEPCPVVIRK-GLDIDKIM 277 Query: 204 RAIS 207 +S Sbjct: 278 MHLS 281 >1jcu_A Conserved protein MTH1692; mixed alpha-beta structure, structural genomics; NMR {Methanothermobacterthermautotrophicus} SCOP: d.115.1.1 Length = 208 Score = 136 bits (343), Expect = 6e-33 Identities = 53/204 (25%), Positives = 92/204 (45%), Gaps = 10/204 (4%) Query: 1 MQIMSITDSN----ALRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPA 56 M I IT N L +A ++ G + PT+T+YGL V++ + A+RRL+ +K R Sbjct: 1 MLIRKITRKNPSPDVLEEAISVMEGGGIVIYPTDTIYGLGVNALDEDAVRRLFRVKGRSP 60 Query: 57 MNPLICHVSDISMVKKHASVDPLSLHLAKLFWPGPLTLVLDLLSTTDIHPLSTANLKTAC 116 P+ VS + + + + ++ L + PGP T+VL+ I + T Sbjct: 61 HKPVSICVSCVDEIPRFSRPSGDAMELMERILPGPYTVVLE--RNELIPDVITGGSSRVG 118 Query: 117 FRVPCGFTKKLIETYGHPLAIPSANRSGQISITNVKHILSSSICKEIPLIIDGGISKIGL 176 RVP + I P+ SAN SG+ ++ I+ + L++D G Sbjct: 119 IRVPDDEICRRIAAR-FPVTATSANISGKPPSPRLEEIV--RDLDAVDLVLDAGDCLDME 175 Query: 177 ESTIVNVQCEKKVRILRPGGLEIE 200 ST++++ R+LR G ++ Sbjct: 176 PSTVIDL-TVNPPRVLRRGKGPLD 198 >1k7j_A Protein YCIO, protein TF1; structural genomics, X-RAY crystallography, putative translation factor, PSI, protein structure initiative; 1.40A {Escherichia coli} SCOP: d.115.1.1 PDB: 1kk9_A Length = 206 Score = 129 bits (324), Expect = 1e-30 Identities = 46/204 (22%), Positives = 84/204 (41%), Gaps = 8/204 (3%) Query: 2 QIMSITDSN----ALRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAM 57 Q I N + +A E + G I PT++ Y L + A+ R+ I++ P Sbjct: 3 QFFYIHPDNPQQRLINQAVEIVRKGGVIVYPTDSGYALGCKIEDKNAMERICRIRQLPDG 62 Query: 58 NPLICHVSDISMVKKHASVDPLSLHLAKLFWPGPLTLVLDLLSTTDIHPLSTANLKTACF 117 + D+S + ++ VD ++ L K PG T +L + L KT Sbjct: 63 HNFTLMCRDLSELSTYSFVDNVAFRLMKNNTPGNYTFILK-GTKEVPRRLLQEKRKTIGM 121 Query: 118 RVP-CGFTKKLIETYGHPLAIPSANRSGQISITNVKHILSSSICKEIPLIIDGGISKIGL 176 RVP + L+E G P+ S G + + + K++ LII GG Sbjct: 122 RVPSNPIAQALLEALGEPMLSTSLMLPGSEFTESDPEEIKDRLEKQVDLIIHGGYLG-QK 180 Query: 177 ESTIVNVQCEKKVRILRPGGLEIE 200 +T++++ + ++R G +++ Sbjct: 181 PTTVIDL-TDDTPVVVREGVGDVK 203 >1hru_A YRDC gene product; protein folding, structural genomics, RNA, SUA5, PSI, protein structure initiative, midwest center for structural genomics; 2.00A {Escherichia coli} SCOP: d.115.1.1 Length = 188 Score = 121 bits (304), Expect = 3e-28 Identities = 48/187 (25%), Positives = 75/187 (40%), Gaps = 8/187 (4%) Query: 8 DSNALRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAMNPLICHVSDI 67 +A+ A + L+ IA PTE V+G+ D + TA+ RL E+K+RP LI ++ Sbjct: 6 QRDAIAAAIDVLNEERVIAYPTEAVFGVGCDPDSETAVMRLLELKQRPVDKGLILIAANY 65 Query: 68 SMVKKHASVDPLS---LHLAKLFWPGPLTLVLDLLSTTDIHPLSTANLKTACFRVP-CGF 123 +K + L+ WPGP+T V +T T + RV Sbjct: 66 EQLKPYIDDTMLTDVQRETIFSRWPGPVTFVFPAPAT--TPRWLTGRFDSLAVRVTDHPL 123 Query: 124 TKKLIETYGHPLAIPSANRSGQISITNVKHILSSSICKEIPLIIDGGISKIGLESTIVNV 183 L + YG PL SAN SG V + + P++ ++ S I + Sbjct: 124 VVALCQAYGKPLVSTSANLSGLPPCRTVDEVR-AQFGAAFPVVPGETGGRLN-PSEIRDA 181 Query: 184 QCEKKVR 190 + R Sbjct: 182 LTGELFR 188 >2yv4_A Hypothetical protein PH0435; alpha and beta proteins (A+B), SUA5 domain, structural genomics, NPPSFA; 2.00A {Pyrococcus horikoshii OT3} Length = 105 Score = 67.2 bits (164), Expect = 4e-12 Identities = 22/101 (21%), Positives = 41/101 (40%), Gaps = 9/101 (8%) Query: 231 APRSQVRL----RAIHVNPREALIRFGNVPIKNI-----ENAIISLNLSKTGKLKEAAFN 281 AP ++V + R L++ K + E+ ++E A N Sbjct: 1 APNAEVIVVEGPREKVKGKITELVKELKERGKKVGVIGSESYNADEFFFLGSSVEEVAKN 60 Query: 282 LFNYMKIADDSGASSIAFSSIPNHGLGIAINNRLERAAAPR 322 LF ++ D +G + + GLG+A+ NRL +A+ + Sbjct: 61 LFKALRYMDKAGVDVVIAEGVEERGLGLAVMNRLRKASGYK 101 >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 = 63.8 bits (155), Expect = 5e-11 Identities = 86/439 (19%), Positives = 135/439 (30%), Gaps = 183/439 (41%) Query: 12 LRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAMNPLICHVSDISMVK 71 L++ +F LP PTE G A D PT L + +VS Sbjct: 33 LQE--QFN-KILPE--PTE---GFAADDE-PTTPAELV------GK--FLGYVSS----- 70 Query: 72 KHASVDPLSLHLAKLFWPGPLTLVL---------DLLSTTDIHPLSTANLKTACFRVPCG 122 V+P G VL L DIH L A L Sbjct: 71 ---LVEPSK--------VGQFDQVLNLCLTEFENCYLEGNDIHAL-AAKL-LQENDTTLV 117 Query: 123 FTKKLIETY-------------GHPLAIPSANRSGQISIT-------NVKHILSSSIC-- 160 TK+LI+ Y A+ A G + N Sbjct: 118 KTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDD------YFE 171 Query: 161 --KEI-----PLIIDGGISKIG--LESTIVNVQCEKKVRILRPGGLEIET-LKRAISV-E 209 +++ L+ D I L I +K + GL I L+ + + Sbjct: 172 ELRDLYQTYHVLVGDL-IKFSAETLSELIRTTLDAEK---VFTQGLNILEWLENPSNTPD 227 Query: 210 LEYCVDETSTPQS-P--GMLK-SHYA---------PRSQVRLR---------------AI 241 +Y + S P S P G+++ +HY P ++R AI Sbjct: 228 KDYLL---SIPISCPLIGVIQLAHYVVTAKLLGFTPG-ELRSYLKGATGHSQGLVTAVAI 283 Query: 242 ---------HVNPREAL-IRF--G----------NVPIKNIENAI----------ISL-N 268 V+ R+A+ + F G ++P +E+++ +S+ N Sbjct: 284 AETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISN 343 Query: 269 LSKTGKLKE--AAFN------------LFNYMKIADDSGASSIAFSSIPN--HGLGIAIN 312 L++ ++++ N L N GA ++ S P +GL N Sbjct: 344 LTQE-QVQDYVNKTNSHLPAGKQVEISLVN--------GAKNLVVSGPPQSLYGL----N 390 Query: 313 NRLERAAAPRNQSQ-RIVP 330 L +A AP Q RI P Sbjct: 391 LTLRKAKAPSGLDQSRI-P 408 Score = 48.4 bits (115), Expect = 2e-06 Identities = 43/263 (16%), Positives = 83/263 (31%), Gaps = 111/263 (42%) Query: 4 M-SITDSNAL-RKACE-FLD---AGLP----IAI-------------PTETVYGLAVDSR 40 M SI++ L ++ + +++ + LP + I P +++YGL + R Sbjct: 338 MLSISN---LTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLR 394 Query: 41 NPTA--------I----RRLYEIKKR--PAMNPLICHVSDISMVKKHASVDPLSLHLAKL 86 A I R+L + R P +P H S L Sbjct: 395 KAKAPSGLDQSRIPFSERKL-KFSNRFLPVASPF--H----------------SHLLVP- 434 Query: 87 FWPGPLTLVLDLLSTTDIHPLSTANLKTACFRVPCGFTKKLIETY-GHPLAIPSANRSGQ 145 L+ L ++ + +++ + +T+ G L R Sbjct: 435 ----ASDLINKDLVKNNV-SFNAKDIQIPVY-----------DTFDGSDL------RVLS 472 Query: 146 ISITNVKHILSSSICKEIPL------------IID---GGISKIGLESTIVNVQCE-KKV 189 SI+ + I + P+ I+D GG S +G + + + V Sbjct: 473 GSIS---ERIVDCIIRL-PVKWETTTQFKATHILDFGPGGASGLG---VLTHRNKDGTGV 525 Query: 190 RILRPGGLEIETLKRAISVELEY 212 R++ G TL + + Sbjct: 526 RVIVAG-----TLDINPDDDYGF 543 Score = 37.6 bits (87), Expect = 0.004 Identities = 35/182 (19%), Positives = 61/182 (33%), Gaps = 42/182 (23%) Query: 74 ASVDPLSLHLAKLFWPGPLTLVLDLLSTTDIHPLSTANLKTACFRVPCGFTKKLIETYGH 133 S PL+L G L VL L+ T S L+ F K L E Sbjct: 4 YSTRPLTLSH------GSLEHVL-LVPTASFFIASQ--LQEQ-------FNKILPE---- 43 Query: 134 PLAIPSANRSGQISITNVKHILSSSICKEIPLIID-GGISKIGLESTIVNV---QCEKKV 189 P+ + T ++ + + SK+G ++N+ + E Sbjct: 44 ----PTEGFAADDEPTTPAELVGKFLG----YVSSLVEPSKVGQFDQVLNLCLTEFEN-- 93 Query: 190 RILRPGGLEIETLKRAISVELEYCVDETSTPQSPGMLKSHYAPRSQVRLRAIHVNPREAL 249 L G +I L + E ++T+ ++ ++K++ R + R AL Sbjct: 94 CYLE--GNDIHALAAKLLQE-----NDTTLVKTKELIKNYITARIMAK-RPFDKKSNSAL 145 Query: 250 IR 251 R Sbjct: 146 FR 147 >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 = 36.1 bits (82), Expect = 0.011 Identities = 10/28 (35%), Positives = 16/28 (57%), Gaps = 7/28 (25%) Query: 274 KLKEAAFNLFNYMKIADDSGASSIAFSS 301 KL +A+ L+ ADDS A ++A + Sbjct: 24 KL-QASLKLY-----ADDS-APALAIKA 44 Score = 27.3 bits (59), Expect = 4.6 Identities = 10/50 (20%), Positives = 14/50 (28%), Gaps = 27/50 (54%) Query: 8 DSNALRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAM 57 + AL+K L A L +LY PA+ Sbjct: 18 EKQALKK----LQASL-----------------------KLYADDSAPAL 40 >1yt3_A Ribonuclease D, RNAse D; exoribonuclease, exonuclease, hydrolase, tRNA processing, hydrolase,translation; 1.60A {Escherichia coli} SCOP: a.60.8.3 a.60.8.3 c.55.3.5 Length = 375 Score = 29.5 bits (65), Expect = 0.93 Identities = 17/89 (19%), Positives = 26/89 (29%), Gaps = 21/89 (23%) Query: 1 MQIMSITDSNALRKACEFLDAGLPIAIPTETVYGLAVDSRNPTAIRRLYEIKKRPAMNPL 60 M IT +AL CE + A IA+ TE P Sbjct: 1 MNYQMITTDDALASLCEAVRAFPAIALDTEF------VRTRT--------------YYPQ 40 Query: 61 ICHVSDISMVKKHASVDPLSLHLAKLFWP 89 + + + + A +DPL + Sbjct: 41 LGLIQ-LFDGEHLALIDPLGITDWSPLKA 68 >2hl0_A Threonyl-tRNA synthetase; translation, editing, aminoacyl-tRNA synthetase, enzyme mechanism, enantioselectivity, ligase; HET: A3S; 1.86A {Pyrococcus abyssi} PDB: 2hkz_A 1y2q_A* 2hl2_A* 2hl1_A* Length = 143 Score = 26.6 bits (59), Expect = 7.2 Identities = 9/21 (42%), Positives = 11/21 (52%), Gaps = 1/21 (4%) Query: 117 FRVPCGFTKKL-IETYGHPLA 136 + P G+ K I GHPLA Sbjct: 113 GKAPFGYYKAFKISCKGHPLA 133 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 0.135 0.389 Gapped Lambda K H 0.267 0.0528 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 2,736,923 Number of extensions: 124917 Number of successful extensions: 280 Number of sequences better than 10.0: 1 Number of HSP's gapped: 263 Number of HSP's successfully gapped: 15 Length of query: 330 Length of database: 5,693,230 Length adjustment: 93 Effective length of query: 237 Effective length of database: 3,438,538 Effective search space: 814933506 Effective search space used: 814933506 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: 57 (26.2 bits)