RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781015|ref|YP_003065428.1| hypothetical protein CLIBASIA_04585 [Candidatus Liberibacter asiaticus str. psy62] (78 letters) >gnl|CDD|100095 cd05802, GlmM, GlmM is a bacterial phosphoglucosamine mutase (PNGM) that belongs to the alpha-D-phosphohexomutase superfamily. It is required for the interconversion of glucosamine-6-phosphate and glucosamine-1-phosphate in the biosynthetic pathway of UDP-N-acetylglucosamine, an essential precursor to components of the cell envelope. In order to be active, GlmM must be phosphorylated, which can occur via autophosphorylation or by the Ser/Thr kinase StkP. GlmM functions in a classical ping-pong bi-bi mechanism with glucosamine-1,6-diphosphate as an intermediate. Other members of the alpha-D-phosphohexomutase superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four domains with a centrally located active site formed by four loops, one from each domain. All four domains are included in this alignment model.. Length = 434 Score = 25.1 bits (56), Expect = 4.0 Identities = 8/27 (29%), Positives = 14/27 (51%), Gaps = 2/27 (7%) Query: 45 KDKGITFKVEKVGDQH--NKILLKEYS 69 K+ GI KVGD++ ++L + Sbjct: 291 KELGIKLVRTKVGDRYVLEEMLKHGAN 317 >gnl|CDD|88445 cd05690, S1_RPS1_repeat_ec5, S1_RPS1_repeat_ec5: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.. Length = 69 Score = 24.1 bits (52), Expect = 9.0 Identities = 7/17 (41%), Positives = 11/17 (64%) Query: 9 LSNALWNQTGKHPSPIF 25 +S+ W Q +HPS I+ Sbjct: 30 ISDISWTQRVRHPSEIY 46 >gnl|CDD|146115 pfam03315, SDH_beta, Serine dehydratase beta chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway. Length = 148 Score = 24.0 bits (53), Expect = 9.5 Identities = 4/32 (12%), Positives = 14/32 (43%), Gaps = 2/32 (6%) Query: 31 QSYRIFLGSGSEV--SKDKGITFKVEKVGDQH 60 + ++ L + + ++ I F +++ H Sbjct: 81 EEGKLNLAGEHSIPFAPERDIVFHFKEILPFH 112 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.318 0.135 0.419 Gapped Lambda K H 0.267 0.0812 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 949,732 Number of extensions: 38682 Number of successful extensions: 81 Number of sequences better than 10.0: 1 Number of HSP's gapped: 81 Number of HSP's successfully gapped: 4 Length of query: 78 Length of database: 6,263,737 Length adjustment: 48 Effective length of query: 30 Effective length of database: 5,226,505 Effective search space: 156795150 Effective search space used: 156795150 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 (21.7 bits) S2: 51 (23.3 bits)