RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780196|ref|YP_003064609.1| hypothetical protein CLIBASIA_00405 [Candidatus Liberibacter asiaticus str. psy62] (125 letters) >gnl|CDD|146462 pfam03840, SecG, Preprotein translocase SecG subunit. Length = 74 Score = 57.1 bits (139), Expect = 1e-09 Identities = 23/74 (31%), Positives = 38/74 (51%), Gaps = 6/74 (8%) Query: 2 QIFLMVVHLIVVVGLVCVILIQSSD----SSAFGSSSNFT--SVRSTAHSLGRFTAILAF 55 L+V+H+IV + L+ ++L+Q AFG ++ + R L + TA+LA Sbjct: 1 YTILLVLHVIVAILLIILVLLQPGKGAGLGGAFGGGASQSLFGSRGARGFLTKLTAVLAV 60 Query: 56 FFFATSIALGMISR 69 FF S+AL +S Sbjct: 61 LFFVLSLALAYLSS 74 >gnl|CDD|31505 COG1314, SecG, Preprotein translocase subunit SecG [Intracellular trafficking and secretion]. Length = 86 Score = 51.4 bits (123), Expect = 7e-08 Identities = 21/77 (27%), Positives = 37/77 (48%), Gaps = 5/77 (6%) Query: 1 MQIFLMVVHLIVVVGLVCVILIQSSDSSAFGS-----SSNFTSVRSTAHSLGRFTAILAF 55 M L+V+ ++V + L+ ++L+Q + G+ S R + L R TAILA Sbjct: 1 MMTLLLVILIVVALALIILVLLQRGKGAGLGASFGGGSGQLFGARGVENFLTRTTAILAV 60 Query: 56 FFFATSIALGMISRYTS 72 FF S+ L +++ Sbjct: 61 LFFIISLVLALLNSKKG 77 >gnl|CDD|110998 pfam02055, Glyco_hydro_30, O-Glycosyl hydrolase family 30. Length = 495 Score = 27.6 bits (61), Expect = 1.1 Identities = 10/25 (40%), Positives = 15/25 (60%) Query: 60 TSIALGMISRYTSTRYKDNMHRSLV 84 T ALG +RYT++R +HR + Sbjct: 28 TFPALGQAARYTTSRSGARLHRDVG 52 >gnl|CDD|37777 KOG2566, KOG2566, KOG2566, Beta-glucocerebrosidase [Carbohydrate transport and metabolism]. Length = 518 Score = 26.9 bits (59), Expect = 1.7 Identities = 10/25 (40%), Positives = 15/25 (60%) Query: 60 TSIALGMISRYTSTRYKDNMHRSLV 84 IA G + YTS+R +HRS++ Sbjct: 52 GFIASGKAAVYTSSRSGARLHRSVI 76 >gnl|CDD|173863 cd08498, PBP2_NikA_DppA_OppA_like_2, The substrate-binding component of an uncharacterized ABC-type nickel/dipeptide/oligopeptide-like import system contains the type 2 periplasmic binding fold. This CD represents the substrate-binding domain of an uncharacterized ATP-binding cassette (ABC) type nickel/dipeptide/oligopeptide-like transporter. The oligopeptide-binding protein OppA and the dipeptide-binding protein DppA show significant sequence similarity to NikA, the initial nickel receptor. The DppA binds dipeptides and some tripeptides and is involved in chemotaxis toward dipeptides, whereas the OppA binds peptides of a wide range of lengths (2-35 amino acid residues) and plays a role in recycling of cell wall peptides, which precludes any involvement in chemotaxis. Most of other periplasmic binding proteins are comprised of only two globular subdomains corresponding to domains I and III of the dipeptide/oligopeptide binding proteins. The structural topology of these domains is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase domains. This interaction triggers the ligand translocation across the cytoplasmic membrane energized by ATP hydrolysis. Besides transport proteins, the PBP2 superfamily includes the ligand-binding domains from ionotropic glutamate receptors, LysR-type transcriptional regulators, and unorthodox sensor proteins involved in signal transduction. Length = 481 Score = 26.0 bits (58), Expect = 3.0 Identities = 12/46 (26%), Positives = 23/46 (50%), Gaps = 3/46 (6%) Query: 77 DNMHRSLV---DSIKDQGNDNFGDGSSPKLDSVSAKSSSSVVAGKR 119 + +L+ D K G N G S+P++D++ ++S + KR Sbjct: 396 SSALDALLHTPDPEKGLGAYNRGGYSNPEVDALIEAAASEMDPAKR 441 >gnl|CDD|112263 pfam03438, Pneumo_NS1, Pneumovirus NS1 protein. This non-structural protein is one of two found in pneumoviruses. The protein is about 140 amino acids in length. The NS1 protein appears to be important for efficient replication but not essential. The NS1 protein has been shown by yeast two-hybrid to interact with the viral P protein. This protein is also known as the 1C protein. It has also been shown that NS1 can potently inhibit transcription and RNA replication. Length = 136 Score = 24.9 bits (54), Expect = 6.9 Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 3/36 (8%) Query: 7 VVHLIVVVGLVCVILIQSSD---SSAFGSSSNFTSV 39 V+H I + G+V + +I SSD ++ + +NFTS+ Sbjct: 45 VIHTIKLNGIVFIHIITSSDICPNNDIINKANFTSM 80 >gnl|CDD|176490 cd08760, Cyt_b561_FRRS1_like, Eukaryotic cytochrome b(561), including the FRRS1 gene product. Cytochrome b(561), as found in eukaryotes, similar to and including the human FRRS1 gene product (ferric-chelate reductase 1), also called SDR-2 (stromal cell-derived receptor 2). This family comprises a variety of domain architectures, many of which contain dopamine beta-monooxygenase (DOMON) domains. The protein might act as a ferric-chelate reductase, catalyzing the reduction of Fe(3+) to Fe(2+), such as associated with the transport of iron from the endosome to the cytoplasm. It is assumed that this protein uses ascorbate as the electron donor. Belongs to the cytochrome b(561) family, which are secretory vesicle-specific electron transport proteins. Cytochromes b(561) are integral membrane proteins that bind two heme groups non-covalently, and may have six alpha-helical trans-membrane segments. Length = 191 Score = 24.6 bits (54), Expect = 8.5 Identities = 7/32 (21%), Positives = 11/32 (34%) Query: 52 ILAFFFFATSIALGMISRYTSTRYKDNMHRSL 83 +LA LG++ +N H L Sbjct: 77 LLAVLLAIAGFVLGIVLVQGGGGSLNNAHAIL 108 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 0.320 0.129 0.347 Gapped Lambda K H 0.267 0.0662 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,257,743 Number of extensions: 55386 Number of successful extensions: 206 Number of sequences better than 10.0: 1 Number of HSP's gapped: 203 Number of HSP's successfully gapped: 32 Length of query: 125 Length of database: 6,263,737 Length adjustment: 82 Effective length of query: 43 Effective length of database: 4,491,799 Effective search space: 193147357 Effective search space used: 193147357 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 (21.9 bits) S2: 51 (23.6 bits)