RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780906|ref|YP_003065319.1| hypothetical protein CLIBASIA_04025 [Candidatus Liberibacter asiaticus str. psy62] (96 letters) >gnl|CDD|173058 PRK14594, rimM, 16S rRNA-processing protein RimM; Provisional. Length = 166 Score = 25.5 bits (56), Expect = 3.2 Identities = 18/57 (31%), Positives = 27/57 (47%), Gaps = 8/57 (14%) Query: 12 FITGMILSSCGDTLSDSKQHNKINNTKNHLDLLFPIDDSHNQKPTEKKPNTSSIKIK 68 F+ G+ILSS G + K+ + N+ + N K KK N SSI++K Sbjct: 2 FVKGIILSSYG-----INGYAKVKSISNNFCDFI---NLKNNKLVLKKSNCSSIEVK 50 >gnl|CDD|132636 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli. Length = 360 Score = 25.3 bits (56), Expect = 3.5 Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 1/45 (2%) Query: 28 SKQHNKINNTKNHL-DLLFPIDDSHNQKPTEKKPNTSSIKIKNNI 71 +K N HL +LL P E +T +IK K +I Sbjct: 282 TKLENADELYNKHLGNLLSPPCLDDKFNLPELVFHTFTIKEKTDI 326 >gnl|CDD|150837 pfam10225, DUF2215, Uncharacterized conserved protein (DUF2215). This entry is the central 200 residues of a family of proteins conserved from worms to humans. The function is unknown. Length = 247 Score = 24.3 bits (53), Expect = 6.4 Identities = 5/20 (25%), Positives = 9/20 (45%) Query: 9 ILFFITGMILSSCGDTLSDS 28 + + G++L LS S Sbjct: 14 VFVLVLGIVLFLLAPLLSRS 33 >gnl|CDD|131606 TIGR02555, OrgA_MxiK, type III secretion apparatus protein OrgA/MxiK. This gene is found in type III secretion operons and has been shown to be essential for the invasion phenotype in Salmonella and a component of the secretion apparatus. The protein is known as OrgA in Salmonella due to its oxygen-dependent expression pattern in which low-oxygen levels up-regulate the gene. In Shigella the ghene is called MxiK and has been shown to be sessential for the proper assembly of the secretion needle complex. Length = 185 Score = 24.4 bits (53), Expect = 6.5 Identities = 6/17 (35%), Positives = 7/17 (41%) Query: 41 LDLLFPIDDSHNQKPTE 57 L+LLFP P Sbjct: 143 LNLLFPDFLEGLLTPLP 159 >gnl|CDD|183230 PRK11613, folP, dihydropteroate synthase; Provisional. Length = 282 Score = 23.9 bits (52), Expect = 8.4 Identities = 9/28 (32%), Positives = 15/28 (53%) Query: 17 ILSSCGDTLSDSKQHNKINNTKNHLDLL 44 IL+ D+ SD HN + + H +L+ Sbjct: 20 ILNVTPDSFSDGGTHNSLIDAVKHANLM 47 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 0.313 0.132 0.406 Gapped Lambda K H 0.267 0.0768 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 1,509,879 Number of extensions: 74898 Number of successful extensions: 95 Number of sequences better than 10.0: 1 Number of HSP's gapped: 95 Number of HSP's successfully gapped: 14 Length of query: 96 Length of database: 5,994,473 Length adjustment: 64 Effective length of query: 32 Effective length of database: 4,611,561 Effective search space: 147569952 Effective search space used: 147569952 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 bits) S2: 50 (23.0 bits)