RPS-BLAST 2.2.22 [Sep-27-2009] Database: mmdb70 33,805 sequences; 4,956,049 total letters Searching..................................................done Query= gi|254780239|ref|YP_003064652.1| 30S ribosomal protein S13 [Candidatus Liberibacter asiaticus str. psy62] (122 letters) >3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast ribosome, ribonucleoprotein particle, macromolecular complex; 9.40A {Oryza sativa} (M:) Length = 145 Score = 116 bits (292), Expect = 1e-27 Identities = 48/111 (43%), Positives = 60/111 (54%), Gaps = 12/111 (10%) Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 RI GV IP KRV +L YIHGIG S+ I L + L E EVI +R+ Sbjct: 46 CIRIGGVEIPNHKRVEYSLQYIHGIGRSRSRQILLDLNFDN-KVTKDLSEEEVIILRK-- 102 Query: 61 EQDYQVEGDLRRTVAMNIKRLMDLGCYRGLRHRRGLPVRGQRTHTNARTRK 111 +R + I+RL ++ CYRG+RH+ GLPVRGQRT N RT K Sbjct: 103 ---------EKRFNRVAIERLKEIRCYRGIRHKLGLPVRGQRTKNNCRTLK 144 >2zkq_m 40S ribosomal protein S18E; protein-RNA complex, 40S ribosomal subunit, ribosomal protein/RNA complex; 8.70A {Canis familiaris} PDB: 1s1h_M (m:1-88) Length = 88 Score = 87.8 bits (218), Expect = 4e-19 Identities = 17/75 (22%), Positives = 34/75 (45%), Gaps = 3/75 (4%) Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 + R+ NI +++ A+ I G+G + + + K I +R +L E EV ++ + Sbjct: 12 ILRVLNTNIDGRRKIAFAITAIKGVGRRYAHVVLRKADIDLTKRAGELTEDEVERVITIM 71 Query: 61 EQDYQVEGD---LRR 72 + Q + L R Sbjct: 72 QNPRQYKIPDWFLNR 86 >2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6; tRNA-binding, rRNA-binding, metal-binding, zinc-finger, translation; HET: TM2 PAR; 2.5A {Thermus thermophilus} (M:1-64) Length = 64 Score = 82.3 bits (204), Expect = 2e-17 Identities = 31/64 (48%), Positives = 42/64 (65%) Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 MARIAGV IPR KRV AL YI+GIG +++ K I P RV L E+EV+++R+ + Sbjct: 1 MARIAGVEIPRNKRVDVALTYIYGIGKARAKEALEKTGINPATRVKDLTEAEVVRLREYV 60 Query: 61 EQDY 64 E + Sbjct: 61 ENTW 64 >3i1m_M 30S ribosomal protein S13; ribosome structure, protein-RNA complex, ribonucleoprotein, ribosomal protein, RNA-binding, rRNA-binding, antibiotic resistance; 3.19A {Escherichia coli k-12} PDB: 1vs7_M* 3e1a_F 3e1c_F 1vs5_M 3i1o_M 3i1q_M 3i1s_M 3i1z_M 3i21_M 2qal_M* 1p6g_M 1p87_M 2aw7_M 2avy_M 2i2u_M 2i2p_M* 2qan_M* 2qb9_M* 2qbb_M* 2qbd_M ... (M:1-63) Length = 63 Score = 78.1 bits (193), Expect = 3e-16 Identities = 22/62 (35%), Positives = 35/62 (56%) Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 MARIAG+NIP K V AL I+G+G S+ I I + ++ +L E ++ +R + Sbjct: 1 MARIAGINIPDHKHAVIALTSIYGVGKTRSKAILAAAGIAEDVKISELSEGQIDTLRDEV 60 Query: 61 EQ 62 + Sbjct: 61 AK 62 >2zbk_B Type 2 DNA topoisomerase 6 subunit B; DNA binding protein, decatenation, ATPase, drug design, DNA-binding, magnesium, metal-binding; HET: RDC; 3.56A {Sulfolobus shibatae} (B:229-310) Length = 82 Score = 75.5 bits (186), Expect = 3e-15 Identities = 10/72 (13%), Positives = 25/72 (34%), Gaps = 4/72 (5%) Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAI 60 + + + IG ++ I + P ++V L E E+ ++ + Sbjct: 13 IKILINNLKRDYTIKEFLVNEFQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVET- 71 Query: 61 EQDYQVEGDLRR 72 ++ + D R Sbjct: 72 ---FKKDEDFRS 80 >2pff_B Fatty acid synthase subunit beta; fatty acid synthase, acyl-carrier-protein, beta-ketoacyl reductase, beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces cerevisiae} (B:1772-1800,B:1916-2006) Length = 120 Score = 31.7 bits (72), Expect = 0.038 Identities = 8/27 (29%), Positives = 18/27 (66%), Gaps = 2/27 (7%) Query: 73 TVA--MNIKRLMDLGCYRGLRHRRGLP 97 ++A M+I+ L+++ YRG+ + +P Sbjct: 1 SLADVMSIESLVEVVFYRGMTMQVAVP 27 >3gzu_A Inner capsid protein VP2; 7RP, DLP, metal- binding, virion, zinc, core protein, RNA-binding, icosaderal virus; 3.80A {Rotavirus A} (A:102-180,A:753-767) Length = 94 Score = 27.3 bits (60), Expect = 0.66 Identities = 14/36 (38%), Positives = 20/36 (55%) Query: 40 PPERRVHQLVESEVIQIRQAIEQDYQVEGDLRRTVA 75 R ++V+SE I AI QD + EG +RR +A Sbjct: 10 KNSRDAGKVVDSETASICDAIFQDEETEGAVRRFIA 45 >3fqi_A Protein DOM3Z, DOM-3 homolog Z; hydrolase, protein binding; HET: EPE; 2.01A {Mus musculus} PDB: 3fqj_A* (A:) Length = 417 Score = 25.1 bits (54), Expect = 3.8 Identities = 5/35 (14%), Positives = 9/35 (25%) Query: 88 RGLRHRRGLPVRGQRTHTNARTRKKFGKGGVARKR 122 H + + H R K+ + K Sbjct: 4 SHHHHHHSSGLVPRSGHMEPRGTKRKAEKTEVEKP 38 >1k82_A Formamidopyrimidine-DNA glycosylase; protein-DNA complex, DNA repair, beta sandwich, zinc finger, helix two-turns helix, hydrolase/DNA complex; HET: PED; 2.10A {Escherichia coli} (A:129-225) Length = 97 Score = 24.7 bits (54), Expect = 4.7 Identities = 9/55 (16%), Positives = 20/55 (36%), Gaps = 3/55 (5%) Query: 11 RAKRVVRAL---CYIHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 + + L + G+G + + I P+R L +E + + I+ Sbjct: 21 KKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKA 75 >1mu5_A Type II DNA topoisomerase VI subunit B; GHKL ATPase, helix two-turns helix; 2.00A {Sulfolobus shibatae} (A:230-311) Length = 82 Score = 24.3 bits (53), Expect = 6.6 Identities = 8/41 (19%), Positives = 19/41 (46%) Query: 22 IHGIGFKSSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 IG ++ I + P ++V L E E+ ++ + ++ Sbjct: 34 FQSIGDTTADKILELAGLKPNKKVKNLTEEEITRLVETFKK 74 >3ip3_A Oxidoreductase, putative; structural genomics, PSI-2, protein structure initiative, NEW YORK SGX research center for structural genomics; 2.14A {Thermotoga maritima} (A:130-337) Length = 208 Score = 24.2 bits (51), Expect = 7.0 Identities = 6/52 (11%), Positives = 13/52 (25%), Gaps = 4/52 (7%) Query: 40 PPERRVHQLVES----EVIQIRQAIEQDYQVEGDLRRTVAMNIKRLMDLGCY 87 P +LV E+ + D + + +G + Sbjct: 4 PHFLTAKKLVSEGAVGEIRLVNTQKSYKLGQRPDFYKKRETYGGTIPWVGIH 55 >1w36_C RECC, exodeoxyribonuclease V gamma chain; recombination, helicase, hydrolase, DNA repair; HET: DNA; 3.1A {Escherichia coli} (C:463-584) Length = 122 Score = 24.0 bits (52), Expect = 7.6 Identities = 7/34 (20%), Positives = 15/34 (44%) Query: 29 SSQDICNKLAIPPERRVHQLVESEVIQIRQAIEQ 62 S+D+ L +P + E + +RQ + + Sbjct: 4 VSEDVLALLDVPVLAARFDITEEGLRYLRQWVNE 37 >1bg6_A N-(1-D-carboxylethyl)-L-norvaline dehydrogenase; L) stereospecific opine dehydrogenase, oxidoreductase; 1.80A {Arthrobacter} (A:196-359) Length = 164 Score = 24.0 bits (52), Expect = 8.2 Identities = 7/39 (17%), Positives = 13/39 (33%) Query: 1 MARIAGVNIPRAKRVVRALCYIHGIGFKSSQDICNKLAI 39 + R V P V+ + + F+ KL + Sbjct: 113 LGRAVNVPTPLIDAVLDLISSLIDTDFRKEGRTLEKLGL 151 >3e1s_A Exodeoxyribonuclease V, subunit RECD; alpha and beta protein, ATP-binding, nucleotide-binding, hydrolase; 2.20A {Deinococcus radiodurans} PDB: 3gp8_A 3gpl_A* (A:1-149) Length = 149 Score = 23.6 bits (51), Expect = 8.6 Identities = 7/34 (20%), Positives = 12/34 (35%), Gaps = 2/34 (5%) Query: 19 LCYIHGIGFKSSQDICNKLAIPP--ERRVHQLVE 50 L + GIGF ++ + RR+ Sbjct: 46 LTEVEGIGFLTADKLWQARGGALDDPRRLTAAAV 79 >1xd7_A YWNA; structural genomics, protein structure initiative, winged helix DNA binding, hypothetical protein, PSI; 2.30A {Bacillus subtilis subsp} (A:) Length = 145 Score = 23.7 bits (51), Expect = 9.1 Identities = 10/58 (17%), Positives = 21/58 (36%), Gaps = 3/58 (5%) Query: 11 RAKRVVRALCYIHGIGFKSSQDICNKLAIPP---ERRVHQLVESEVIQIRQAIEQDYQ 65 R + L I SS+ I + + P R + L +++++ R + Sbjct: 7 RLAVAIHILSLISMDEKTSSEIIADSVNTNPVVVRRMISLLKKADILTSRAGVPGASL 64 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 0.326 0.141 0.416 Gapped Lambda K H 0.267 0.0413 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 33805 Number of Hits to DB: 946,051 Number of extensions: 39683 Number of successful extensions: 321 Number of sequences better than 10.0: 1 Number of HSP's gapped: 319 Number of HSP's successfully gapped: 25 Length of query: 122 Length of database: 4,956,049 Length adjustment: 73 Effective length of query: 49 Effective length of database: 2,488,284 Effective search space: 121925916 Effective search space used: 121925916 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 50 (23.9 bits)