RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780244|ref|YP_003064657.1| 30S ribosomal protein S5 [Candidatus Liberibacter asiaticus str. psy62] (199 letters) >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* ... (E:) Length = 167 Score = 137 bits (347), Expect = 8e-34 Identities = 76/159 (47%), Positives = 109/159 (68%), 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 AMEKARRNMINV-ALNNGTLQHPVKGVHTGSRVFMQPASEGTGIIAGGAMRAVLEVAGVH 121 Query: 134 DVVAKSIGSSNPHNVIRATFEVLRSQSHPRDVANRRGIK 172 +V+AK+ GS+NP NV+RAT + L + + P VA +RG Sbjct: 122 NVLAKAYGSTNPINVVRATIDGLENMNSPEMVAAKRGKS 160 >2vqe_E 30S ribosomal protein S5; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (E:1-143) Length = 143 Score = 125 bits (314), Expect = 6e-30 Identities = 59/142 (41%), Positives = 83/142 (58%), Gaps = 1/142 (0%) Query: 18 RDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEA 77 + ++++ I R + GGRRF F LVVVGD + +VG A EVP AV+KA Sbjct: 2 PETDFEEKMILIRRTARMQAGGRRFRFGALVVVGDRQGRVGLGFGKAPEVPLAVQKAGYY 61 Query: 78 AKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVA 137 A+RNM+ V L T+ H+ GA K++++ A GTGVIAG RA+ E+ G+ D++ Sbjct: 62 ARRNMVEVPL-QNGTIPHEIEVEFGASKIVLKPAAPGTGVIAGAVPRAILELAGVTDILT 120 Query: 138 KSIGSSNPHNVIRATFEVLRSQ 159 K +GS NP N+ AT E LR Sbjct: 121 KELGSRNPINIAYATMEALRQL 142 >2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (e:82-179) Length = 98 Score = 90.6 bits (225), Expect = 1e-19 Identities = 19/87 (21%), Positives = 34/87 (39%), Gaps = 4/87 (4%) Query: 90 GRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNP-HNV 148 T+ GR G+ V + A GTG+++ + + + G+ D + G + N Sbjct: 4 PHTVPCKVTGRSGSVPVRLIPAPRGTGIVSAPVPKKLLMMAGIDDCYTSARGCTATLGNF 63 Query: 149 IRATFEVLR---SQSHPRDVANRRGIK 172 +ATF+ + S P K Sbjct: 64 AKATFDAISKTYSYLTPDLWKETVFTK 90 >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 (E:75-162) Length = 88 Score = 86.8 bits (215), Expect = 2e-18 Identities = 19/84 (22%), Positives = 38/84 (45%), Gaps = 4/84 (4%) Query: 90 GRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNP-HNV 148 +L G+ G+ V + A G+G++A A++ + ++ G+ DV +S G + N Sbjct: 3 PHSLATKTTGKCGSVTVRLIPAPRGSGIVASPAVKKLLQLAGVEDVYTQSNGKTRTLENT 62 Query: 149 IRATFEVL---RSQSHPRDVANRR 169 ++A F + P A + Sbjct: 63 LKAAFVAIGNTYGFLTPNLWAEQP 86 >3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (E:221-289) Length = 69 Score = 86.7 bits (215), Expect = 2e-18 Identities = 28/67 (41%), Positives = 42/67 (62%) Query: 92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRA 151 T H +GA +V++R A GTGVIAGGA+R V E+ G+ + + K +GS+N N RA Sbjct: 2 TFPHRNEADYGAARVMLRPAAPGTGVIAGGAVRTVLEMAGVENALGKQLGSNNALNNARA 61 Query: 152 TFEVLRS 158 T +++ Sbjct: 62 TIVAVQT 68 >1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} (A:79-150) Length = 72 Score = 86.3 bits (214), Expect = 2e-18 Identities = 34/68 (50%), Positives = 51/68 (75%) Query: 92 TLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPHNVIRA 151 T+ H+ +G GAG++I++ A GTGVIAGG RAV E+ G+ D+++KSIGS+ P N++RA Sbjct: 2 TIPHEVIGHFGAGEIILKPASEGTGVIAGGPARAVLELAGISDILSKSIGSNTPINMVRA 61 Query: 152 TFEVLRSQ 159 TF+ L+ Sbjct: 62 TFDGLKQL 69 >1pkp_A Ribosomal protein S5; 2.80A {Geobacillus stearothermophilus} (A:1-78) Length = 78 Score = 78.6 bits (194), Expect = 6e-16 Identities = 36/76 (47%), Positives = 49/76 (64%) Query: 13 QNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVR 72 + + +R+VA+NRV+ + GGRR FS LVVVGD VGF A+EVPEA+R Sbjct: 2 RRINPNKLELEERVVAVNRVAKVVKGGRRLRFSALVVVGDKNGHVGFGTGKAQEVPEAIR 61 Query: 73 KATEAAKRNMISVSLL 88 KA E AK+N+I V ++ Sbjct: 62 KAIEDAKKNLIEVPIV 77 >3bbn_E Ribosomal protein S5; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Spinacea oleracea} (E:1-220) Length = 220 Score = 71.7 bits (175), Expect = 7e-14 Identities = 28/87 (32%), Positives = 48/87 (55%) Query: 1 MAQKERSQRDNWQNREERDNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFA 60 K+ + + +E+ + + +V + RV+ + GG+ F +VVVGD K +VG Sbjct: 131 SKIKKATGFGSKSKKEKIRDGFEENVVQVRRVTKVVKGGKHMRFRAIVVVGDKKGQVGVG 190 Query: 61 HSTAREVPEAVRKATEAAKRNMISVSL 87 A+EV AV+KA A+RN+I+V + Sbjct: 191 VGKAKEVVSAVQKAAVDARRNIITVPM 217 >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 (E:1-74) Length = 74 Score = 66.3 bits (162), Expect = 2e-12 Identities = 23/72 (31%), Positives = 34/72 (47%) Query: 21 SIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKR 80 + D ++ I V G+R F +VVVGD+ VG TA+EV A+R AK Sbjct: 1 GLQDEVMNIKPVQKQTRAGQRTRFKAVVVVGDSNGHVGLGIKTAKEVAGAIRAGIIIAKL 60 Query: 81 NMISVSLLDGRT 92 ++I + T Sbjct: 61 SVIPIRRGYWGT 72 >2zkq_e 40S ribosomal protein S2E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} (e:1-81) Length = 81 Score = 62.9 bits (153), Expect = 3e-11 Identities = 20/65 (30%), Positives = 31/65 (47%) 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 85 +++ V Sbjct: 69 SIVPV 73 >2of5_H Leucine-rich repeat and death domain-containing protein; death domain complex, apoptosis; 3.20A {Homo sapiens} (H:) Length = 118 Score = 29.2 bits (65), Expect = 0.36 Identities = 10/59 (16%), Positives = 19/59 (32%), Gaps = 2/59 (3%) Query: 124 RAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRS--QSHPRDVANRRGIKHSLLQARR 180 AV LG+ + I ++ +L S + + +L Q+ R Sbjct: 28 PAVALHLGVSYREVQRIRHEFRDDLDEQIRHMLFSWAERQAGQPGAVGLLVQALEQSDR 86 >3go2_A Putative L-alanine-DL-glutamate epimerase; structural genomics, isomerase, PSI-2, protein structure initiative; 1.70A {Burkholderia xenovorans LB400} PDB: 2oo6_A (A:1-110,A:381-409) Length = 139 Score = 28.0 bits (62), Expect = 1.0 Identities = 19/147 (12%), Positives = 46/147 (31%), Gaps = 26/147 (17%) Query: 25 RIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAAKRNMIS 84 ++V+++ + V + + VG++ V E + ++ Sbjct: 4 KVVSVDTLCCDAGWRNY----HFVKLTTDEGIVGWSEFDEGFGSPGVTAVIEQLGKRLVG 59 Query: 85 VSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIG--- 141 S+++ + TG + I A+ + D AK++ Sbjct: 60 ASVMEHERFFAE----------AYCLTRPATGGVVSEGIGAI--ENALLDAKAKTLNVPC 107 Query: 142 -------SSNPHNVIRATFEVLRSQSH 161 ++P V+ + RS+ H Sbjct: 108 YELEEAILAHPPKVMGGLLQYKRSEGH 134 >2fxu_A Alpha-actin-1, actin, alpha skeletal muscle; actin complexed to bistramide A, structural protein; HET: HIC ATP BID; 1.35A {Oryctolagus cuniculus} (A:138-182,A:263-352) Length = 135 Score = 26.0 bits (57), Expect = 3.1 Identities = 15/72 (20%), Positives = 24/72 (33%), Gaps = 16/72 (22%) Query: 76 EAAKRNMISVSLLDGRTLHHDGVGRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDV 135 ++ +V + +G L H IMR +AG G E G+H+ Sbjct: 17 DSGDGVTHNVPIYEGYALPHA----------IMRLDLAGQPSFIG------MESAGIHET 60 Query: 136 VAKSIGSSNPHN 147 SI + Sbjct: 61 TYNSIMKCDIDI 72 >2nvo_A RO sixty-related protein, RSR; alpha helical repeats, VON willebrand factor A domain, beta- sheet, RNA binding protein; 1.89A {Deinococcus radiodurans} (A:289-358) Length = 70 Score = 26.3 bits (58), Expect = 3.2 Identities = 12/60 (20%), Positives = 16/60 (26%) Query: 19 DNSIVDRIVAINRVSTALPGGRRFAFSVLVVVGDTKSKVGFAHSTAREVPEAVRKATEAA 78 D++ V ++ AL GR L G V A E A Sbjct: 3 DSATVQAVIERLTDPAALKRGRIHPLDALKARLVYAQGQGVRGKGTWLPVPRVVDALEEA 62 >1fad_A Protein (FADD protein); apoptosis, death domain; NMR {Mus musculus} (A:) Length = 99 Score = 25.2 bits (55), Expect = 5.6 Identities = 9/59 (15%), Positives = 22/59 (37%), Gaps = 3/59 (5%) Query: 124 RAVCEVLGMHDVVAKSIGSSNPHNVIRATFEVLRS--QSHPRDVANRRGIKHSLLQARR 180 + + L + + I P ++ E L+ + ++ A+ G+ +L R Sbjct: 29 KRLARELKVSEAKMDGIEEKYPRSLSERVRESLKVWKNAEKKN-ASVAGLVKALRTCRL 86 >2hpi_A DNA polymerase III alpha subunit; POL-beta-like nucleotidyltransferase fold; HET: DNA; 3.00A {Thermus aquaticus} PDB: 2hpm_A* 3e0d_A* (A:451-623) Length = 173 Score = 25.2 bits (55), Expect = 6.1 Identities = 8/48 (16%), Positives = 17/48 (35%), Gaps = 5/48 (10%) Query: 99 GRHGAGKVIMRSAMAGTGVIAGGAIRAVCEVLGMHDVVAKSIGSSNPH 146 G ++ ++A A++ V V G+ A+ + P Sbjct: 35 GEDKVAQIGTFGSLASKA-----ALKDVARVYGIPHKKAEELAKLIPV 77 Database: mmdb70 Posted date: Jun 20, 2010 3:12 AM Number of letters in database: 4,956,049 Number of sequences in database: 33,805 Lambda K H 0.316 0.129 0.359 Gapped Lambda K H 0.267 0.0653 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 1,426,987 Number of extensions: 60684 Number of successful extensions: 214 Number of sequences better than 10.0: 1 Number of HSP's gapped: 210 Number of HSP's successfully gapped: 35 Length of query: 199 Length of database: 4,956,049 Length adjustment: 84 Effective length of query: 115 Effective length of database: 2,116,429 Effective search space: 243389335 Effective search space used: 243389335 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: 52 (24.0 bits)