RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780305|ref|YP_003064718.1| hypothetical protein CLIBASIA_00950 [Candidatus Liberibacter asiaticus str. psy62] (95 letters) >gnl|CDD|31101 COG0758, Smf, Predicted Rossmann fold nucleotide-binding protein involved in DNA uptake [DNA replication, recombination, and repair / Intracellular trafficking and secretion]. Length = 350 Score = 45.0 bits (106), Expect = 4e-06 Identities = 19/82 (23%), Positives = 33/82 (40%), Gaps = 1/82 (1%) Query: 6 IEQNFFSSQSDTNHTKNINITHYPEYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVVY 65 I++ S + + +N Y + + +L + P ID + TG+ V Sbjct: 269 IKEGAKLVTSAEDILEELNALLVLLYPY-TFLALLANLGDEPKEIDRLASCTGLTIAQVL 327 Query: 66 LVLLELDLAGRLCHHPEGKVSL 87 LLEL+L G++ G L Sbjct: 328 AWLLELELEGKVKRLGGGYYRL 349 >gnl|CDD|143853 pfam00071, Ras, Ras family. Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See pfam00009 pfam00025, pfam00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices. Length = 162 Score = 25.5 bits (57), Expect = 3.1 Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%) Query: 40 KQSLNNVPIHIDDIIHHTGIEAPVVYLVLLELDLA 74 + S NV +++I+ H P+V LV + DL Sbjct: 84 RDSFENVKKWLEEILRHADDNVPIV-LVGNKCDLE 117 >gnl|CDD|73064 cd02658, Peptidase_C19B, A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.. Length = 311 Score = 25.3 bits (55), Expect = 4.4 Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 6/75 (8%) Query: 5 QIEQNFFSSQSDTNHTKNINITHYPEYTQCERVRIKQSLNNVPIHIDDIIHHTGIEAPVV 64 IE + + T TK +P+Y R + N VP +D I P Sbjct: 192 TIEDFCSTCKEKTTATKTTGFKTFPDYLVINMKRFQLLENWVPKKLDVPIDVPEELGPGK 251 Query: 65 YLVLLELDLAGRLCH 79 Y +L + H Sbjct: 252 Y------ELIAFISH 260 >gnl|CDD|143409 cd07090, ALDH_F9_TMBADH, NAD+-dependent 4-trimethylaminobutyraldehyde dehydrogenase, ALDH family 9A1. NAD+-dependent, 4-trimethylaminobutyraldehyde dehydrogenase (TMABADH, EC=1.2.1.47), also known as aldehyde dehydrogenase family 9 member A1 (ALDH9A1) in humans, is a cytosolic tetramer which catalyzes the oxidation of gamma-aminobutyraldehyde involved in 4-aminobutyric acid (GABA) biosynthesis and also oxidizes betaine aldehyde (gamma-trimethylaminobutyraldehyde) which is involved in carnitine biosynthesis. Length = 457 Score = 25.0 bits (55), Expect = 4.8 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%) Query: 52 DIIHHTGIEAPVVYLVLLELDLAGRLCHHPE-GKVSLTMHLPS 93 +I+ G+ V +V + LC HP+ KVS T +P+ Sbjct: 164 EILTEAGLPDGVFNVVQGGGETGQLLCEHPDVAKVSFTGSVPT 206 >gnl|CDD|37096 KOG1885, KOG1885, KOG1885, Lysyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]. Length = 560 Score = 24.9 bits (54), Expect = 5.7 Identities = 8/13 (61%), Positives = 11/13 (84%) Query: 23 INITHYPEYTQCE 35 I++TH PE+T CE Sbjct: 308 IDLTHNPEFTTCE 320 >gnl|CDD|63868 cd04399, RhoGAP_fRGD2, RhoGAP_fRGD2: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of fungal RGD2-like proteins. Yeast Rgd2 is a GAP protein for Cdc42 and Rho5. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.. Length = 212 Score = 24.5 bits (53), Expect = 7.6 Identities = 10/37 (27%), Positives = 14/37 (37%), Gaps = 4/37 (10%) Query: 39 IKQSLNNVPIHIDDIIHHTGIEAPVVY----LVLLEL 71 ++ LN ++I E V L LLEL Sbjct: 56 LRNLLNKPKKPDKEVIILKKFEPSTVASVLKLYLLEL 92 >gnl|CDD|29807 cd00496, PheRS_alpha_core, Phenylalanyl-tRNA synthetase (PheRS) alpha chain catalytic core domain. PheRS belongs to class II aminoacyl-tRNA synthetases (aaRS) based upon its structure and the presence of three characteristic sequence motifs. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. While class II aaRSs generally aminoacylate the 3'-OH ribose of the appropriate tRNA, PheRS is an exception in that it attaches the amino acid at the 2'-OH group, like class I aaRSs. PheRS is an alpha-2/ beta-2 tetramer.. Length = 218 Score = 23.9 bits (52), Expect = 8.8 Identities = 8/23 (34%), Positives = 13/23 (56%) Query: 22 NINITHYPEYTQCERVRIKQSLN 44 I+ TH PE+ Q E + + + L Sbjct: 94 EIDATHLPEFHQIEGLVVDKGLT 116 >gnl|CDD|29820 cd00775, LysRS_core, Lys_tRNA synthetase (LysRS) class II core domain. Class II LysRS is a dimer which attaches a lysine to the 3' OH group of ribose of the appropriate tRNA. Its assignment to class II aaRS is based upon its structure and the presence of three characteristic sequence motifs in the core domain. It is found in eukaryotes as well as some prokaryotes and archaea. However, LysRS belongs to class I aaRS's in some prokaryotes and archaea. The catalytic core domain is primarily responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate.. Length = 329 Score = 24.0 bits (52), Expect = 9.7 Identities = 7/13 (53%), Positives = 10/13 (76%) Query: 23 INITHYPEYTQCE 35 I++TH PE+T E Sbjct: 91 IDLTHNPEFTMIE 103 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 0.136 0.415 Gapped Lambda K H 0.267 0.0832 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,194,543 Number of extensions: 53153 Number of successful extensions: 108 Number of sequences better than 10.0: 1 Number of HSP's gapped: 108 Number of HSP's successfully gapped: 9 Length of query: 95 Length of database: 6,263,737 Length adjustment: 63 Effective length of query: 32 Effective length of database: 4,902,370 Effective search space: 156875840 Effective search space used: 156875840 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 (21.8 bits) S2: 51 (23.2 bits)