RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18 [Candidatus Liberibacter asiaticus str. psy62] (83 letters) >gnl|CDD|178997 PRK00391, rpsR, 30S ribosomal protein S18; Reviewed. Length = 79 Score = 94.9 bits (237), Expect = 4e-21 Identities = 37/72 (51%), Positives = 49/72 (68%) Query: 11 RRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIK 70 RR R+K C + IDYKD+ LL +F+S+RGKI+P RI+ S K QR+LA AIK Sbjct: 7 RRRFFRRKKVCRFCAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQLATAIK 66 Query: 71 RARYLGLIAYVN 82 RAR+L L+ YV+ Sbjct: 67 RARFLALLPYVD 78 >gnl|CDD|161738 TIGR00165, S18, ribosomal protein S18. This ribosomal small subunit protein is found in all eubacteria so far, as well as in chloroplasts. YER050C from Saccharomyces cerevisiae and a related protein from Caenorhabditis elegans appear to be homologous and may represent mitochondrial forms. The trusted cutoff is set high enough that these two candidate S18 proteins are not categorized automatically. Length = 70 Score = 76.3 bits (188), Expect = 2e-15 Identities = 37/66 (56%), Positives = 48/66 (72%) Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76 R+K C + +G IDYKD+ LL +F+S+RGKI+P RI+ S K QR LA+AIKRARYL Sbjct: 4 RKKYCRFTAEGIQFIDYKDLDLLKKFISERGKILPRRITGTSAKYQRRLARAIKRARYLA 63 Query: 77 LIAYVN 82 L+ YV Sbjct: 64 LLPYVK 69 >gnl|CDD|184031 PRK13401, PRK13401, 30S ribosomal protein S18; Provisional. Length = 82 Score = 66.3 bits (162), Expect = 1e-12 Identities = 27/77 (35%), Positives = 40/77 (51%) Query: 6 PTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQREL 65 R + K L G +DYKD LL F+S RGKI R++ ++ ++QR++ Sbjct: 1 MAAKPARKGPTKAKKNLLDSLGIESVDYKDTALLRTFISDRGKIRSRRVTGLTVQQQRQV 60 Query: 66 AKAIKRARYLGLIAYVN 82 A AIK AR + L+ Y Sbjct: 61 ATAIKNAREMALLPYPG 77 >gnl|CDD|184030 PRK13400, PRK13400, 30S ribosomal protein S18; Provisional. Length = 147 Score = 58.5 bits (141), Expect = 4e-10 Identities = 30/65 (46%), Positives = 40/65 (61%) Query: 17 RRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLG 76 +RK C + RIDYKD L R++S RGKI P R + + QR LA AIKRAR++ Sbjct: 21 KRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTCARHQRALANAIKRARFIA 80 Query: 77 LIAYV 81 L+ +V Sbjct: 81 LMPFV 85 >gnl|CDD|162733 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase, type 2. Isopentenyl-diphosphate delta-isomerase (IPP isomerase) interconverts isopentenyl diphosphate and dimethylallyl diphosphate. This model represents the type 2 enzyme. FMN, NADPH, and Mg2+ are required by this form, which lacks homology to the type 1 enzyme (TIGR02150). IPP is precursor to many compounds, including enzyme cofactors, sterols, and isoprenoids. Length = 333 Score = 28.4 bits (64), Expect = 0.42 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 10/55 (18%) Query: 29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVS--HKK----QRELAKAIKRARYLGL 77 P I+ DI L FL +R K P I++++ ++ R LA+A AR LG+ Sbjct: 34 PEINLDDIDLTTEFLGKRLK-APFYINAMTGGSEEAGKINRNLARA---ARELGI 84 >gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA; Provisional. Length = 362 Score = 26.8 bits (59), Expect = 1.4 Identities = 26/83 (31%), Positives = 41/83 (49%), Gaps = 7/83 (8%) Query: 1 MAEVAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHK 60 E+ P L + +R + P K R++ D RLL RFL++ I P + S+V ++ Sbjct: 282 EQELFACPDLAVRIRYRSRPIPCRVK---RLE--DGRLLVRFLAEASAIAPGQ-SAVFYE 335 Query: 61 KQRELAKA-IKRARYLGLIAYVN 82 +R L A I R +GL+ N Sbjct: 336 GRRVLGGAFIASQRGIGLVIEQN 358 >gnl|CDD|184388 PRK13909, PRK13909, putative recombination protein RecB; Provisional. Length = 910 Score = 25.3 bits (56), Expect = 3.6 Identities = 11/39 (28%), Positives = 15/39 (38%), Gaps = 1/39 (2%) Query: 34 KDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRA 72 D + FL ++ I SS Q E KA+ A Sbjct: 482 DDALEIKEFLQEQFGIKAVTESSAKLINQPE-VKALIEA 519 >gnl|CDD|162863 TIGR02456, treS_nterm, trehalose synthase. Trehalose synthase interconverts maltose and alpha, alpha-trehalose by transglucosylation. This is one of at least three mechanisms for biosynthesis of trehalose, an important and widespread compatible solute. However, it is not driven by phosphate activation of sugars and its physiological role may tend toward trehalose degradation. This view is accentuated by numerous examples of fusion to a probable maltokinase domain. The sequence region described by this model is found both as the whole of a trehalose synthase and as the N-terminal region of a larger fusion protein that includes trehalose synthase activity. Several of these fused trehalose synthases have a domain homologous to proteins with maltokinase activity from Actinoplanes missouriensis and Streptomyces coelicolor (PubMed:15378530). Length = 539 Score = 25.1 bits (55), Expect = 3.7 Identities = 15/42 (35%), Positives = 19/42 (45%), Gaps = 5/42 (11%) Query: 2 AEVAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFL 43 A AP P +R N+ RR+ PL D + I LL L Sbjct: 324 AAYAPDPRMRINLGIRRRLAPLLDN-----DRRRIELLTALL 360 >gnl|CDD|184750 PRK14568, vanB, D-alanine--D-lactate ligase; Provisional. Length = 343 Score = 25.1 bits (55), Expect = 4.1 Identities = 12/24 (50%), Positives = 16/24 (66%) Query: 49 IVPSRISSVSHKKQRELAKAIKRA 72 IVP+ IS+ + +E AKAI RA Sbjct: 259 IVPADISAEERSRVQETAKAIYRA 282 >gnl|CDD|180527 PRK06319, PRK06319, DNA topoisomerase I/SWI domain fusion protein; Validated. Length = 860 Score = 24.8 bits (54), Expect = 5.0 Identities = 13/41 (31%), Positives = 22/41 (53%) Query: 31 IDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKR 71 + YK +L+R L +R + R+ SV+ K + KAI+ Sbjct: 145 VGYKISPILSRKLQRRSGVSAGRVQSVALKLVVDREKAIEA 185 >gnl|CDD|132173 TIGR03129, one_C_dehyd_B, formylmethanofuran dehydrogenase subunit B. Members of this largely archaeal protein family are subunit B of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdB) from molybdenum-containing (FmdB) forms of this enzyme. Length = 421 Score = 24.6 bits (54), Expect = 6.6 Identities = 12/43 (27%), Positives = 23/43 (53%), Gaps = 2/43 (4%) Query: 34 KDIRLLNRFLSQ-RGK-IVPSRISSVSHKKQRELAKAIKRARY 74 D L++ + RGK P ++ + +K ELA+ +K A++ Sbjct: 201 SDYELISALRAVLRGKEPQPEEVAGIPKEKILELAEILKNAKF 243 >gnl|CDD|132362 TIGR03319, YmdA_YtgF, conserved hypothetical protein YmdA/YtgF. Length = 514 Score = 24.1 bits (53), Expect = 9.3 Identities = 11/31 (35%), Positives = 17/31 (54%) Query: 42 FLSQRGKIVPSRISSVSHKKQRELAKAIKRA 72 L Q G+I P+RI + K +E+ AI+ Sbjct: 266 KLIQDGRIHPARIEEMVEKATKEVDNAIREE 296 >gnl|CDD|183293 PRK11730, fadB, multifunctional fatty acid oxidation complex subunit alpha; Reviewed. Length = 715 Score = 24.1 bits (53), Expect = 9.8 Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 6/27 (22%) Query: 60 KKQRELAKAIKRARYLGL------IAY 80 KK + AK +K+A LG IAY Sbjct: 304 KKLAKDAKPVKQAAVLGAGIMGGGIAY 330 Database: CddB Posted date: Feb 4, 2011 9:54 PM Number of letters in database: 5,994,473 Number of sequences in database: 21,608 Lambda K H 0.323 0.136 0.386 Gapped Lambda K H 0.267 0.0769 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,379,710 Number of extensions: 73446 Number of successful extensions: 172 Number of sequences better than 10.0: 1 Number of HSP's gapped: 172 Number of HSP's successfully gapped: 27 Length of query: 83 Length of database: 5,994,473 Length adjustment: 52 Effective length of query: 31 Effective length of database: 4,870,857 Effective search space: 150996567 Effective search space used: 150996567 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 (22.0 bits) S2: 50 (23.0 bits)