RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5 [Candidatus Liberibacter asiaticus str. psy62] (199 letters) >3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} Length = 308 Score = 172 bits (437), Expect = 4e-44 Identities = 62/170 (36%), Positives = 96/170 (56%) Query: 3 QKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHS 62 K+ + + +E+ + + +V + RV+ + GG+ F +VVVGD K +VG Sbjct: 133 IKKATGFGSKSKKEKIRDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVGVG 192 Query: 63 TAREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGA 122 A+EV AV+KA A+RN+I+V + T H +GA +V++R A GTGVIAGGA Sbjct: 193 KAKEVVSAVQKAAVDARRNIITVPMTKYLTFPHRNEADYGAARVMLRPAAPGTGVIAGGA 252 Query: 123 IRAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 +R V E+ G+ + + K +GS+N N RAT +++ DVA RGI Sbjct: 253 VRTVLEMAGVENALGKQLGSNNALNNARATIVAVQTMRQFSDVARDRGIP 302 >3ofo_E 30S ribosomal protein S5; protein biosynthesis, ribosomes, RNA, tRNA, transfer, eryThr ketolide, macrolide, antibiotic, EXIT, peptidyl; 3.10A {Escherichia coli} PDB: 3fih_E* 3iy8_E 2wwl_E 3ofp_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* 2qbj_E* 2qou_E* 2qow_E* ... Length = 150 Score = 152 bits (384), Expect = 7e-38 Identities = 75/147 (51%), Positives = 105/147 (71%), Gaps = 1/147 (0%) Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83 ++++A+NRVS + GGR F+F+ L VVGD +VGF + AREVP A++KA E A+RNMI Sbjct: 4 EKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQKAMEKARRNMI 63 Query: 84 SVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143 +V+L + TL H G H +V M+ A GTG+IAGGA+RAV EV G+H+V+AK+ GS+ Sbjct: 64 NVAL-NNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVHNVLAKAYGST 122 Query: 144 NPHNVIRATFEVLRSQSHPRDVANRRG 170 NP NV+RAT + L + + P VA +RG Sbjct: 123 NPINVVRATIDGLENMNSPEMVAAKRG 149 >3i1m_E 30S ribosomal protein S5; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_E* 1vs5_E 3i1o_E 3i1q_E 3i1s_E 3i1z_E 3i21_E 2qal_E* 1p6g_E 1p87_E 2aw7_E 2avy_E 2i2u_E 2i2p_E* 2qan_E* 2qb9_E* 2qbb_E* 2qbd_E 2qbf_E 2qbh_E* ... Length = 167 Score = 148 bits (376), Expect = 7e-37 Identities = 76/159 (47%), Positives = 110/159 (69%), Gaps = 1/159 (0%) Query: 14 NREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRK 73 + E++ + ++++A+NRVS + GGR F+F+ L VVGD +VGF + AREVP A++K Sbjct: 3 HIEKQAGELQEKLIAVNRVSKTVKGGRIFSFTALTVVGDGNGRVGFGYGKAREVPAAIQK 62 Query: 74 ATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133 A E A+RNMI+V+L + TL H G H +V M+ A GTG+IAGGA+RAV EV G+H Sbjct: 63 AMEKARRNMINVAL-NNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVH 121 Query: 134 DVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 +V+AK+ GS+NP NV+RAT + L + + P VA +RG Sbjct: 122 NVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS 160 >1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} SCOP: d.14.1.1 d.50.1.2 PDB: 1eg0_B 1dv4_E* 1qd7_D Length = 150 Score = 142 bits (359), Expect = 6e-35 Identities = 71/136 (52%), Positives = 98/136 (72%), Gaps = 1/136 (0%) Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83 +R+VA+NRV+ + GGRR FS LVVVGD VGF A+EVPEA+RKA E AK+N+I Sbjct: 13 ERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIRKAIEDAKKNLI 72 Query: 84 SVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSS 143 V + G T+ H+ +G GAG++I++ A GTGVIAGG RAV E+ G+ D+++KSIGS+ Sbjct: 73 EVPI-VGTTIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSN 131 Query: 144 NPHNVIRATFEVLRSQ 159 P N++RATF+ L+ Sbjct: 132 TPINMVRATFDGLKQL 147 >3jyv_E 40S ribosomal protein S2; eukaryotic ribosome, RACK1 protein, flexible fitting; HET: 2MG H2U M2G OMC OMG YYG PSU 5MC 7MG 5MU 1MA; 8.90A {Thermomyces lanuginosus} PDB: 1s1h_E Length = 162 Score = 137 bits (347), Expect = 1e-33 Identities = 42/157 (26%), Positives = 72/157 (45%), Gaps = 11/157 (7%) Query: 24 DRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMI 83 D ++ I V G+R F +VVVGD+ VG TA+EV A+R AK ++I Sbjct: 4 DEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKLSVI 63 Query: 84 SV-------SLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVV 136 + +L +L G+ G+ V + A G+G++A A++ + ++ G+ DV Sbjct: 64 PIRRGYWGTNLGQPHSLATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVY 123 Query: 137 AKSIGSSN-PHNVIRATFEVL---RSQSHPRDVANRR 169 +S G + N ++A F + P A + Sbjct: 124 TQSNGKTRTLENTLKAAFVAIGNTYGFLTPNLWAEQP 160 >2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} SCOP: i.1.1.3 PDB: 1fka_E 1gix_H* 1hnw_E* 1hnx_E* 1hnz_E* 1hr0_E 1ibk_E* 1ibl_E* 1ibm_E 1jgo_H* 1jgp_H* 1jgq_H* 1ml5_H* 1xmo_E* 1xmq_E* 1xnq_E* 1xnr_E* 1yl4_H 2b64_E* 2b9m_E* ... Length = 162 Score = 136 bits (343), Expect = 4e-33 Identities = 62/154 (40%), Positives = 87/154 (56%), Gaps = 1/154 (0%) Query: 19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAA 78 + ++++ I R + GGRRF F LVVVGD + +VG A EVP AV+KA A Sbjct: 3 ETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYYA 62 Query: 79 KRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAK 138 +RNM+ V L T+ H+ GA K++++ A GTGVIAG RA+ E+ G+ D++ K Sbjct: 63 RRNMVEVPL-QNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILTK 121 Query: 139 SIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 +GS NP N+ AT E LR DV R + Sbjct: 122 ELGSRNPINIAYATMEALRQLRTKADVERLRKGE 155 >2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} Length = 179 Score = 124 bits (313), Expect = 1e-29 Identities = 36/147 (24%), Positives = 63/147 (42%), Gaps = 8/147 (5%) Query: 21 SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKR 80 S+ D ++ I V G+R F V +GD VG ++EV A+R A AK Sbjct: 9 SLKDEVLKIVPVQKQTRAGQRTRFKAFVAIGDHNGHVGLGVKCSKEVATAIRGAIILAKL 68 Query: 81 NMISV-------SLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMH 133 +++ V + T+ GR G+ V + A GTG+++ + + + G+ Sbjct: 69 SIVPVRRGYWGNKIGKPHTVPCKVTGRSGSVPVRLIPAPRGTGIVSAPVPKKLLMMAGID 128 Query: 134 DVVAKSIGSSNP-HNVIRATFEVLRSQ 159 D + G + N +ATF+ + Sbjct: 129 DCYTSARGCTATLGNFAKATFDAISKT 155 >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 = 39.2 bits (91), Expect = 6e-04 Identities = 38/229 (16%), Positives = 63/229 (27%), Gaps = 115/229 (50%) Query: 6 RSQR-------------DNWQNREE--------RDNSI--VDRIVAINRVSTALPGGRRF 42 R D+ +N E + + V +N+ ++ LP G++ Sbjct: 309 RCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDY--VNKTNSHLPAGKQV 366 Query: 43 AFSV------LVVVGDTKSKVGFAHSTARE-----------VPEAVRK------------ 73 S+ LVV G +S G T R+ +P + RK Sbjct: 367 EISLVNGAKNLVVSGPPQSLYGLN-LTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVAS 425 Query: 74 ---------ATEAAKRNM------ISVSLL--------DGRTL----------------- 93 A++ +++ + + DG L Sbjct: 426 PFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIR 485 Query: 94 ---H----------H--D-GVGR-HGAGKVIMRSAMAGTG--VIAGGAI 123 H D G G G G + R+ GTG VI G + Sbjct: 486 LPVKWETTTQFKATHILDFGPGGASGLGVLTHRN-KDGTGVRVIVAGTL 533 Score = 31.8 bits (72), Expect = 0.099 Identities = 15/93 (16%), Positives = 27/93 (29%), Gaps = 38/93 (40%) Query: 125 AV-CEVLGM--------------HD---VVAKSIGSS--------NPHNVIRATFEV-LR 157 V ++LG H V A +I + + I F + +R Sbjct: 250 VVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFIGVR 309 Query: 158 SQ-SHPR---------D-VANRRGIKHSLLQAR 179 ++P D + N G+ +L Sbjct: 310 CYEAYPNTSLPPSILEDSLENNEGVPSPMLSIS 342 >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 = 0.40 Identities = 10/24 (41%), Positives = 12/24 (50%), Gaps = 8/24 (33%) Query: 172 KHSL--LQARRVVSSKSSSYSRDS 193 K +L LQA S K Y+ DS Sbjct: 19 KQALKKLQA----SLKL--YADDS 36 Score = 29.6 bits (65), Expect = 0.45 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 8/34 (23%) Query: 122 AIRAVCEVLGMH-DVVAKSIGSSNPHNVIRATFE 154 A++ + L ++ D S P I+AT E Sbjct: 21 ALKKLQASLKLYAD-------DSAPALAIKATME 47 >3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190 Score = 29.1 bits (64), Expect = 0.62 Identities = 10/33 (30%), Positives = 17/33 (51%), Gaps = 7/33 (21%) Query: 1 MAQ--KERSQRD--NWQNREERD---NSIVDRI 26 M Q +E++++D W R+ N I +RI Sbjct: 108 MEQEWREKAKKDLEEWNQRQSEQVEKNKINNRI 140 >1v77_A PH1877P, hypothetical protein PH1877; RNAse P protein, TIM-barrel, RNA binding protein; 1.80A {Pyrococcus horikoshii} SCOP: c.6.3.2 PDB: 2czv_A* Length = 212 Score = 26.0 bits (57), Expect = 6.0 Identities = 17/134 (12%), Positives = 38/134 (28%), Gaps = 31/134 (23%) Query: 37 PGGRRFAFSVLVVV----GDTKSKVGFAHSTAREVPEAVRKATEAAKRNMISVSLLDGRT 92 R++ V + G H A+ + +++ Sbjct: 86 LRVIRYSIEKGVDAIISPWVNRKDPGIDHVLAK-----------LMVKKNVALGFSLRPL 134 Query: 93 LHHDGVGR----------------HGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVV 136 L+ + R + + + SA V + ++ V+GM Sbjct: 135 LYSNPYERANLLRFMMKAWKLVEKYKVRRFLTSSAQEKWDVRYPRDLISLGVVIGMEIPQ 194 Query: 137 AKSIGSSNPHNVIR 150 AK+ S P +++ Sbjct: 195 AKASISMYPEIILK 208 >1mgt_A MGMT, protein (O6-methylguanine-DNA methyltransferase); DNA repair protein, suicidal enzyme, hyperthermostability; 1.80A {Thermococcus kodakarensis KOD1} SCOP: a.4.2.1 c.55.7.1 Length = 174 Score = 25.7 bits (56), Expect = 7.4 Identities = 14/54 (25%), Positives = 25/54 (46%) Query: 64 AREVPEAVRKATEAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGV 117 A+ + + R A KRN + + R + HDG+G + +G + + GV Sbjct: 116 AKALNTSPRAVGGAMKRNPYPIVVPCHRVVAHDGIGYYSSGIEEKKFLLEIEGV 169 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 0.129 0.359 Gapped Lambda K H 0.267 0.0589 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 1,593,177 Number of extensions: 70578 Number of successful extensions: 221 Number of sequences better than 10.0: 1 Number of HSP's gapped: 212 Number of HSP's successfully gapped: 25 Length of query: 199 Length of database: 5,693,230 Length adjustment: 88 Effective length of query: 111 Effective length of database: 3,559,758 Effective search space: 395133138 Effective search space used: 395133138 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 (21.7 bits) S2: 54 (24.9 bits)