RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780801|ref|YP_003065214.1| hypothetical protein CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62] (222 letters) >1ct5_A Protein (yeast hypothetical protein, selenoMet); TIM barrel, pyridoxal-5'-phosphate, selenomethionine, MAD, structural genomics, PSI; HET: PLP; 2.00A {Saccharomyces cerevisiae} SCOP: c.1.6.2 PDB: 1b54_A* Length = 256 Score = 192 bits (490), Expect = 5e-50 Identities = 66/237 (27%), Positives = 101/237 (42%), Gaps = 22/237 (9%) Query: 3 LGNKLQVFKQKIENSA--ILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60 L + + ++ + A + + L+ VSK+ + I++ G F EN +QE Sbjct: 14 LIAQYESVREVVNAEAKNVHVNENASKILLLVVSKLKPASDIQILYDHGVREFGENYVQE 73 Query: 61 AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSL--FDVIETVSREKTASLLSLEMIK--- 115 +K L D++ FIG LQ+NK ++ + +ET+ K A L+ K Sbjct: 74 LIEKAKLLPD--DIKWHFIGGLQTNKCKDLAKVPNLYSVETIDSLKKAKKLNESRAKFQP 131 Query: 116 QSRFLPVYIQVNTGYEIQKSGIMPNQTKDFV---ILCRQKYQLNVEGLMCIP-----PAM 167 + +Q+NT +E QKSG+ V L + + + GLM I Sbjct: 132 DCNPILCNVQINTSHEDQKSGLNNEAEIFEVIDFFLSEECKYIKLNGLMTIGSWNVSHED 191 Query: 168 GNPKPHFYLLSEIARECK-----LTKLSMGMTRDFELAIASGATSVRIGSGIFGERP 219 F L E ++ KLSMGM+ DF AI G VRIG+ IFG RP Sbjct: 192 SKENRDFATLVEWKKKIDAKFGTSLKLSMGMSADFREAIRQGTAEVRIGTDIFGARP 248 >3cpg_A Uncharacterized protein; unknown protein, TIM barrel, monomer, structural genomics, PSI-2, protein structure initiative; 1.71A {Bifidobacterium adolescentis ATCC15703} Length = 282 Score = 176 bits (448), Expect = 3e-45 Identities = 67/243 (27%), Positives = 101/243 (41%), Gaps = 31/243 (12%) Query: 7 LQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWI 66 + +I + A R SV L+A +K D +I A+ G + EN+ QE K Sbjct: 29 VHRVLDRIAAAEEQAGREAGSVRLLAATKTRDIGEIMAAIDAGVRMIGENRPQEVTAKAE 88 Query: 67 PLRK-------------------EWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTAS 107 L + + IG LQSNK+ +++ + D IE+V A Sbjct: 89 GLARRCAERGFSLGVAGAAPDAAAEHIPFHLIGQLQSNKIGKVLPVVDTIESVDSIDLAE 148 Query: 108 LLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAM 167 +S + + + V ++VN E KSG P + ++GLM I + Sbjct: 149 KISRRAVARGITVGVLLEVNESGEESKSGCDPAHAIRIAQKIGTLDGIELQGLMTIGAHV 208 Query: 168 GNP---KPHFYLLSEIARECK---------LTKLSMGMTRDFELAIASGATSVRIGSGIF 215 + + F L + +LSMGMT D ELAIA G+T VR+G+ IF Sbjct: 209 HDETVIRRGFSHLRKTRDLILASGEPGTDRCRELSMGMTGDMELAIAEGSTIVRVGTAIF 268 Query: 216 GER 218 GER Sbjct: 269 GER 271 >1w8g_A YGGS, hypothetical UPF0001 protein YGGS; structural genomics, hypothetical protein, putative enzyme with PLP-binding domain; HET: PLP ICT; 2.0A {Escherichia coli} Length = 234 Score = 146 bits (370), Expect = 3e-36 Identities = 72/229 (31%), Positives = 109/229 (47%), Gaps = 11/229 (4%) Query: 1 MS-LGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQ 59 M+ + + L + KI +A R + ++L+AVSK + I A+ GQ F EN +Q Sbjct: 1 MNDIAHNLAQVRDKISAAATRCGRSPEEITLLAVSKTKPASAIAEAIDAGQRQFGENYVQ 60 Query: 60 E--AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQS 117 E K + ++ FIG LQSNK + FD T+ R + A+ L+ + + Sbjct: 61 EGVDKIRHFQELGVTGLEWHFIGPLQSNKSRLVAEHFDWCHTIDRLRIATRLNDQRPAEL 120 Query: 118 RFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLL 177 L V IQ+N E KSGI + + + +L + GLM IP F + Sbjct: 121 PPLNVLIQINISDENSKSGIQLAELDELAAAVAELPRLRLRGLMAIPAPESEYVRQFEVA 180 Query: 178 SEIARECK--------LTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218 ++A + LS+GM+ D E AIA+G+T VRIG+ IFG R Sbjct: 181 RQMAVAFAGLKTRYPHIDTLSLGMSDDMEAAIAAGSTMVRIGTAIFGAR 229 >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 = 43.0 bits (101), Expect = 6e-05 Identities = 42/218 (19%), Positives = 67/218 (30%), Gaps = 93/218 (42%) Query: 12 QKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIF-----AENKLQEAKKKWI 66 K NSA+ + + LVA IF ++ +E Sbjct: 138 DKKSNSALFRAVGEGNAQLVA-------------------IFGGQGNTDDYFEE------ 172 Query: 67 PLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQV 126 LR + +G D+I+ + E + L+ V+ Q Sbjct: 173 -LRDLYQTYHVLVG--------------DLIKFSA-ETLSELIRTT----LDAEKVFTQ- 211 Query: 127 NTGYEIQK--SGIMPNQTKDFVILCRQKYQLNVEGLMCIP---PAMGNPKPHFYLLSEIA 181 G I + P+ T D + Y L+ IP P +G + ++A Sbjct: 212 --GLNILEWLEN--PSNTPD------KDY------LLSIPISCPLIG--------VIQLA 247 Query: 182 R---ECKLTKLSMGMTRDFELAIASGATSVRIG-S-GI 214 KL + G R + L GAT G S G+ Sbjct: 248 HYVVTAKLLGFTPGELRSY-L---KGAT----GHSQGL 277 Score = 28.0 bits (62), Expect = 1.6 Identities = 33/158 (20%), Positives = 53/158 (33%), Gaps = 75/158 (47%) Query: 28 VSLVAVSKMVDS---------KKIRVALSCG---QVIF-----AENKLQEAKK--KWIP- 67 V+ VA++ DS K I V G + + L+++ + + +P Sbjct: 278 VTAVAIA-ETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPS 336 Query: 68 -------LRKEWDVQLRFIG----SLQSNK-VSEIVSLFD-----VIETVSREKT---AS 107 L +E VQ ++ L + K V +SL + V+ + S Sbjct: 337 PMLSISNLTQE-QVQ-DYVNKTNSHLPAGKQVE--ISLVNGAKNLVV-------SGPPQS 385 Query: 108 L----LSLEMIK------QSR-------------FLPV 122 L L+L K QSR FLPV Sbjct: 386 LYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPV 423 >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 = 29.8 bits (66), Expect = 0.46 Identities = 33/139 (23%), Positives = 57/139 (41%), Gaps = 47/139 (33%) Query: 54 AENKLQEAKKKW-----------IPLRKEWDVQLRFIGSLQSN--KVSEI-VSLFDVIET 99 AE++L+ A+++W PLR G+L + + ++ V+ F T Sbjct: 1298 AESQLRAAQQQWGNDFYKRDPRIAPLR----------GALATYGLTIDDLGVASFHGTST 1347 Query: 100 VSREKTASLLSLEMIKQ-------------SRFLPVYIQ-------VNTGYEIQKSGIMP 139 + +K S EM+K +FL + + +N +I SGI+P Sbjct: 1348 KANDKNESATINEMMKHLGRSEGNPVIGVFQKFLTGHPKGAAGAWMMNGALQILNSGIIP 1407 Query: 140 -NQTKDFV--ILCRQKYQL 155 N+ D V IL + +Y L Sbjct: 1408 GNRNADNVDKILEQFEYVL 1426 >3cpr_A Dihydrodipicolinate synthetase; (beta/alpha)8-barrel fold with A C-terminal alpha-helical segment, amino-acid biosynthesis, cytoplasm; HET: MCL; 2.20A {Corynebacterium glutamicum} Length = 304 Score = 27.5 bits (60), Expect = 2.8 Identities = 10/67 (14%), Positives = 20/67 (29%), Gaps = 2/67 (2%) Query: 106 ASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPP 165 + + + L + +G+ N T+ V L +GL+ + P Sbjct: 63 SPTTTAAEKLE--LLKAVREEVGDRAKLIAGVGTNNTRTSVELAEAAASAGADGLLVVTP 120 Query: 166 AMGNPKP 172 P Sbjct: 121 YYSKPSQ 127 >3noe_A DAP-A, dihydrodipicolinate synthase; Lys biosynthesis pathway, lyase; 2.95A {Pseudomonas aeruginosa} Length = 292 Score = 26.8 bits (59), Expect = 3.9 Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 2/65 (3%) Query: 106 ASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPP 165 ++ L +E Q + + G +G N T++ V L + + + P Sbjct: 48 SATLDVEEHIQ--VVRRVVDQVKGRIPVIAGTGANSTREAVALTEAAKSGGADACLLVTP 105 Query: 166 AMGNP 170 P Sbjct: 106 YYNKP 110 >2zjr_R 50S ribosomal protein L24; ribosome, large ribosomal subunit, ribonucleoprotein, RNA-binding, rRNA-binding, tRNA-binding, methylation; 2.91A {Deinococcus radiodurans} SCOP: b.34.5.1 PDB: 1nwx_S* 1nwy_S* 1sm1_S* 1xbp_S* 2d3o_S 2zjp_R* 2zjq_R 1nkw_S 3cf5_R* 3dll_R* 1pnu_S 1pny_S 1vor_V 1vou_V 1vow_V 1voy_V 1vp0_V Length = 115 Score = 26.6 bits (59), Expect = 4.3 Identities = 9/18 (50%), Positives = 15/18 (83%) Query: 35 KMVDSKKIRVALSCGQVI 52 ++VD KK+RVA++ G+ I Sbjct: 97 QIVDGKKVRVAVASGKTI 114 >3bbo_W Ribosomal protein L24; large ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 191 Score = 26.4 bits (58), Expect = 4.8 Identities = 6/27 (22%), Positives = 16/27 (59%) Query: 38 DSKKIRVALSCGQVIFAENKLQEAKKK 64 D +K+R + G+++ ++ +E + K Sbjct: 154 DVRKVRYLIKTGEIVDTPDRWKEIQNK 180 >3bi8_A Dihydrodipicolinate synthase; TIM-barrel, amino-acid biosynthesis, cytoplasm, diaminopimelate biosynthesis, lyase, lysine biosynthesis; HET: MLT; 1.96A {Clostridium botulinum} PDB: 3ird_A* Length = 291 Score = 26.3 bits (57), Expect = 5.2 Identities = 10/56 (17%), Positives = 18/56 (32%), Gaps = 8/56 (14%) Query: 136 GIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKP-----HFYLLSEIARECKL 186 G N T + + + + V+GL+ I P HF ++ Sbjct: 76 GTGSNNTAASIAMSKWAESIGVDGLLVITPYYNKTTQKGLVKHF---KAVSDAVST 128 >1y0e_A Putative N-acetylmannosamine-6-phosphate 2- epimerase; mannac-6-P epimerase, NANE, structural genomics, protein structure initiative; 1.95A {Staphylococcus aureus subsp} SCOP: c.1.2.5 Length = 223 Score = 26.4 bits (57), Expect = 5.6 Identities = 11/84 (13%), Positives = 24/84 (28%), Gaps = 5/84 (5%) Query: 139 PNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPHFYLLSEIARECKLTKLSMGMTR--- 195 + K+ L + G + F L ++ + ++ G Sbjct: 129 VEEAKNAARLGFDYIGTTLHGYTSYTQGQLLYQNDFQFLKDVLQSVDAKVIAEGNVITPD 188 Query: 196 DFELAIASGATSVRIGSGIFGERP 219 ++ + G +G I RP Sbjct: 189 MYKRVMDLGVHCSVVGGAIT--RP 210 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 26.0 bits (56), Expect = 6.7 Identities = 21/95 (22%), Positives = 36/95 (37%), Gaps = 32/95 (33%) Query: 60 EAKKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRF 119 E+ +KW R+E Q ++ E+ + V+E REK L +QS Sbjct: 85 ESIRKW---REE-----------QRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSE- 129 Query: 120 LPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQ 154 +++K+ I N+ D + YQ Sbjct: 130 -----------QVEKNKI-NNRIAD-----KAFYQ 147 >3ofq_U 50S ribosomal protein L24; protein biosynthesis, ribosomes, RNA, tRNA, transfer, antibi EXIT, peptidyl, ribosomal subunit, large; 3.10A {Escherichia coli} PDB: 2j28_U* 3fik_U 2wwq_U 3ofr_U* 3i1n_U 1vs8_U 1vs6_U 1vt2_U 3i1p_U 3i1r_U 3i1t_U 3i20_U 3i22_U 3kcr_U 3orb_U* 3e1b_O 3e1d_O 2qam_U* 1p85_S 1p86_S ... Length = 102 Score = 25.8 bits (57), Expect = 7.6 Identities = 6/18 (33%), Positives = 9/18 (50%) Query: 35 KMVDSKKIRVALSCGQVI 52 + D KK+R S + I Sbjct: 85 RFEDGKKVRFFKSNSETI 102 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 0.378 Gapped Lambda K H 0.267 0.0697 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,758,281 Number of extensions: 75654 Number of successful extensions: 244 Number of sequences better than 10.0: 1 Number of HSP's gapped: 234 Number of HSP's successfully gapped: 19 Length of query: 222 Length of database: 5,693,230 Length adjustment: 89 Effective length of query: 133 Effective length of database: 3,535,514 Effective search space: 470223362 Effective search space used: 470223362 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: 55 (25.0 bits)