RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780500|ref|YP_003064913.1| hypothetical protein CLIBASIA_01935 [Candidatus Liberibacter asiaticus str. psy62] (159 letters) >gnl|CDD|32737 COG2913, SmpA, Small protein A (tmRNA-binding) [Translation, ribosomal structure and biogenesis]. Length = 147 Score = 46.9 bits (111), Expect = 2e-06 Identities = 29/119 (24%), Positives = 53/119 (44%), Gaps = 6/119 (5%) Query: 37 GSISGASLDMSAISLVSQGSSRSHVIESLGSPSFSILHNGNRSQSFYYVSQKKKWFPVKF 96 G LD A+ + G ++ V+ LG+PS + N +YYV Q+++ Sbjct: 34 DINQGNVLDQDAVDQLKVGMTKDQVLYLLGTPSLVDTFDTNT---WYYVFQQQR--RGVA 88 Query: 97 LSPKIMEYIVLKITFGEKGVVSSVSMERL-PNRRFNPNPHTIPAPIQTADGFLRRLLNP 154 P+I+E L + F + GVV+S+++ + + F T P P + + + N Sbjct: 89 FGPEIVEQKTLTVYFDKDGVVTSIAVYKPADGKAFEAVNRTTPTPGKELTFLQQLVGNR 147 >gnl|CDD|146803 pfam04355, SmpA_OmlA, SmpA / OmlA family. Lipoprotein Bacterial outer membrane lipoprotein, possibly involved in in maintaining the structural integrity of the cell envelope. Lipid attachment site is a conserved N terminal cysteine residue. Sometimes found adjacent to the OmpA domain (pfam00691). Length = 71 Score = 41.4 bits (98), Expect = 1e-04 Identities = 16/77 (20%), Positives = 31/77 (40%), Gaps = 10/77 (12%) Query: 44 LDMSAISLVSQGSSRSHVIESLGSPSFSILHNGNRSQSFYYVSQKKKWFPVKFLSPKIME 103 + + + G ++ V LG+PS N +YYV ++ +E Sbjct: 4 VTQEDVDQLKPGMTKEQVRYLLGTPSLEDTFGPNT---WYYVYNFRR-------GGGAVE 53 Query: 104 YIVLKITFGEKGVVSSV 120 VL + F + G+V ++ Sbjct: 54 QQVLAVYFDDDGLVRNI 70 >gnl|CDD|133174 cd05042, PTKc_Aatyk, Catalytic domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase (Aatyk) subfamily; catalytic (c) domain. The Aatyk subfamily is also referred to as the lemur tyrosine kinase (Lmtk) subfamily. It consists of Aatyk1 (Lmtk1), Aatyk2 (Lmtk2, Brek), Aatyk3 (Lmtk3), and similar proteins. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk proteins are mostly receptor tyr kinases (RTKs) containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 does not contain a transmembrane segment and is a cytoplasmic (or nonreceptor) kinase. Aatyk proteins are classified as tyr kinases based on overall sequence similarity and the phylogenetic tree. However, analysis of catalytic residues suggests that Aatyk proteins may be multispecific kinases, functioning also as serine/threonine kinases. They are involved in neural differentiation, nerve growth factor (NGF) signaling, apoptosis, and spermatogenesis. Length = 269 Score = 31.4 bits (71), Expect = 0.11 Identities = 6/21 (28%), Positives = 16/21 (76%) Query: 83 YYVSQKKKWFPVKFLSPKIME 103 YY+++ P+++L+P+++E Sbjct: 155 YYITKDCHAVPLRWLAPELVE 175 >gnl|CDD|133322 cd04122, Rab14, Rab14 subfamily. Rab14 GTPases are localized to biosynthetic compartments, including the rough ER, the Golgi complex, and the trans-Golgi network, and to endosomal compartments, including early endosomal vacuoles and associated vesicles. Rab14 is believed to function in both the biosynthetic and recycling pathways between the Golgi and endosomal compartments. Rab14 has also been identified on GLUT4 vesicles, and has been suggested to help regulate GLUT4 translocation. In addition, Rab14 is believed to play a role in the regulation of phagocytosis. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic localization. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. Due to the presence of truncated sequences in this CD, the lipid modification site is not available for annotation. Length = 166 Score = 29.4 bits (66), Expect = 0.49 Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 1/35 (2%) Query: 104 YIVLKITFGEKGVVSSVSMERLPNRRFNPN-PHTI 137 YI I G+ GV S + + ++F + PHTI Sbjct: 1 YIFKYIIIGDMGVGKSCLLHQFTEKKFMADCPHTI 35 >gnl|CDD|173646 cd05087, PTKc_Aatyk1_Aatyk3, Catalytic domain of the Protein Tyrosine Kinases, Apoptosis-associated tyrosine kinases 1 and 3. Protein Tyrosine Kinase (PTK) family; Apoptosis-associated tyrosine kinase 1 (Aatyk1) and Aatyk3; catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Aatyk1 and Aatyk3 are members of the Aatyk subfamily of proteins. Aatyk3 is a receptor kinase containing a transmembrane segment and a long C-terminal cytoplasmic tail with a catalytic domain. Aatyk1 has a similar domain arrangement but without the transmembrane segment and is thus, a cytoplasmic (or nonreceptor) kinase. The expression of Aatyk1 (also referred simply as Aatyk) is upregulated during growth arrest and apoptosis in myeloid cells. Aatyk1 has been implicated in neural differentiation, and is a regulator of the Na-K-2Cl cotransporter, a membrane protein involved in cell proliferation and survival, epithelial transport, and blood pressure control. The function of Aatyk3 is still unknown. Length = 269 Score = 27.6 bits (61), Expect = 1.5 Identities = 8/34 (23%), Positives = 22/34 (64%), Gaps = 2/34 (5%) Query: 70 FSILHNGNRSQSFYYVSQKKKWFPVKFLSPKIME 103 + + HN + YYV+ + W P+++++P++++ Sbjct: 144 YGLSHNKYKED--YYVTPDQLWVPLRWIAPELVD 175 >gnl|CDD|112512 pfam03702, UPF0075, Uncharacterized protein family (UPF0075). The proteins is this family are about 370 amino acids long and have no known function. Length = 363 Score = 27.7 bits (62), Expect = 1.6 Identities = 12/32 (37%), Positives = 18/32 (56%) Query: 37 GSISGASLDMSAISLVSQGSSRSHVIESLGSP 68 G +SG SLD +LV G ++ ++ S SP Sbjct: 5 GLMSGTSLDGVDAALVDIGLTKIELLASHSSP 36 >gnl|CDD|34081 COG4372, COG4372, Uncharacterized protein conserved in bacteria with the myosin-like domain [Function unknown]. Length = 499 Score = 27.4 bits (60), Expect = 2.0 Identities = 10/30 (33%), Positives = 12/30 (40%) Query: 125 LPNRRFNPNPHTIPAPIQTADGFLRRLLNP 154 P R+F IPAP Q +DG Sbjct: 426 SPARQFRARRPGIPAPAQNSDGAAPTWSTF 455 >gnl|CDD|37454 KOG2243, KOG2243, KOG2243, Ca2+ release channel (ryanodine receptor) [Signal transduction mechanisms]. Length = 5019 Score = 27.0 bits (59), Expect = 2.8 Identities = 18/92 (19%), Positives = 28/92 (30%), Gaps = 8/92 (8%) Query: 53 SQGSSRSHV------IESLGSPSFSILHNGNRSQSFYYVSQKKKWFPVKFLSPKIMEYIV 106 Q S R++ + S + NG + Y V K FP F + Sbjct: 1505 GQRSGRNNNDLEIGCLVDAAMGLLSFIANGKELGTCYQVEPNTKLFPAVFAQATSPN--L 1562 Query: 107 LKITFGEKGVVSSVSMERLPNRRFNPNPHTIP 138 + G+ +S + NP P P Sbjct: 1563 FQFELGKIKNAMPLSAAIFKSEEKNPVPQCPP 1594 >gnl|CDD|48183 cd03372, TPP_ComE, Thiamine pyrophosphate (TPP) family, ComE subfamily, TPP-binding module; composed of proteins similar to Methanococcus jannaschii sulfopyruvate decarboxylase beta subunit (ComE). M. jannaschii sulfopyruvate decarboxylase (ComDE) is a dodecamer of six alpha (D) subunits and six (E) beta subunits, which catalyzes the decarboxylation of sulfopyruvic acid to sulfoacetaldehyde in the coenzyme M pathway. ComDE requires TPP and divalent metal cation cofactors.. Length = 179 Score = 26.7 bits (59), Expect = 3.2 Identities = 10/36 (27%), Positives = 17/36 (47%) Query: 48 AISLVSQGSSRSHVIESLGSPSFSILHNGNRSQSFY 83 AI + V+ ++G PS + G+R +FY Sbjct: 4 AIKTLIADLKDELVVSNIGFPSKELYAAGDRPLNFY 39 >gnl|CDD|109982 pfam00947, Pico_P2A, Picornavirus core protein 2A. This protein is a protease, involved in cleavage of the polyprotein. Length = 127 Score = 26.2 bits (58), Expect = 4.1 Identities = 8/21 (38%), Positives = 13/21 (61%) Query: 83 YYVSQKKKWFPVKFLSPKIME 103 YY + K++PV F P ++E Sbjct: 45 YYCKSRNKYYPVTFTGPTLIE 65 >gnl|CDD|39713 KOG4513, KOG4513, KOG4513, Phosphoglycerate mutase [Carbohydrate transport and metabolism]. Length = 531 Score = 25.4 bits (55), Expect = 7.2 Identities = 8/32 (25%), Positives = 10/32 (31%) Query: 51 LVSQGSSRSHVIESLGSPSFSILHNGNRSQSF 82 L G H E+ + NG R F Sbjct: 334 LAHNGVRTFHCAETEKFAHVTFFFNGGREGYF 365 >gnl|CDD|173624 cd00192, PTKc, Catalytic domain of Protein Tyrosine Kinases. Protein Tyrosine Kinase (PTK) family, catalytic domain. This PTKc family is part of a larger superfamily that includes the catalytic domains of protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. They can be classified into receptor and non-receptor tyr kinases. PTKs play important roles in many cellular processes including, lymphocyte activation, epithelium growth and maintenance, metabolism control, organogenesis regulation, survival, proliferation, differentiation, migration, adhesion, motility, and morphogenesis. Receptor tyr kinases (RTKs) are integral membrane proteins which contain an extracellular ligand-binding region, a transmembrane segment, and an intracellular tyr kinase domain. RTKs are usually activated through ligand binding, which causes dimerization and autophosphorylation of the intracellular tyr kinase catalytic domain, leading to intracellular signaling. Some RTKs are orphan receptors with no known ligands. Non-receptor (or cytoplasmic) tyr kinases are distributed in different intracellular compartments and are usually multi-domain proteins containing a catalytic tyr kinase domain as well as various regulatory domains such as SH3 and SH2. PTKs are usually autoinhibited and require a mechanism for activation. In many PTKs, the phosphorylation of tyr residues in the activation loop is essential for optimal activity. Aberrant expression of PTKs is associated with many development abnormalities and cancers. Length = 262 Score = 25.2 bits (56), Expect = 8.2 Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 10/41 (24%) Query: 83 YYVSQKKKWFPVKFLSPKIMEYIVLKITFGEK------GVV 117 YY + P+++++P E + I F K GV+ Sbjct: 160 YYRKKTGGKLPIRWMAP---ESLKDGI-FTSKSDVWSFGVL 196 >gnl|CDD|146137 pfam03345, DDOST_48kD, Oligosaccharyltransferase 48 kDa subunit beta. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase EC:2.4.1.119, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This family includes the 48kD-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1. Length = 439 Score = 25.3 bits (56), Expect = 8.2 Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 2/34 (5%) Query: 106 VLKITFGEKGV--VSSVSMERLPNRRFNPNPHTI 137 + K F EKGV V V+ +NP +TI Sbjct: 264 LTKWVFKEKGVLKVGKVTHHLAGEPSYNPEIYTI 297 >gnl|CDD|144920 pfam01504, PIP5K, Phosphatidylinositol-4-phosphate 5-Kinase. This family contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in. The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway. Length = 257 Score = 25.3 bits (56), Expect = 8.5 Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 1/31 (3%) Query: 63 ESLGSPS-FSILHNGNRSQSFYYVSQKKKWF 92 +SL S S L +G +S SF+Y S+ ++ Sbjct: 1 KSLCSLDTLSELSSGGKSGSFFYKSRDGRFI 31 >gnl|CDD|37906 KOG2695, KOG2695, KOG2695, WD40 repeat protein [General function prediction only]. Length = 425 Score = 25.0 bits (54), Expect = 8.6 Identities = 13/53 (24%), Positives = 21/53 (39%), Gaps = 15/53 (28%) Query: 82 FYYVSQKKKWFPVKFLSPKIMEYIVLKITFGEKGVVSSVSMERL-PNRRFNPN 133 +YY S+KK++F + S + + ERL P +RF Sbjct: 10 YYYNSEKKRYFRIS--SG------------QSTPSSNIYTKERLKPGKRFENI 48 >gnl|CDD|31154 COG0812, MurB, UDP-N-acetylmuramate dehydrogenase [Cell envelope biogenesis, outer membrane]. Length = 291 Score = 25.2 bits (55), Expect = 8.8 Identities = 16/60 (26%), Positives = 23/60 (38%), Gaps = 10/60 (16%) Query: 103 EYIVLKITF-GEKGVVSSVS--MERLPNRRFNPNPHTIPAPIQTADGFLRRLLNPNGRSA 159 +VL + F KG + M + RR P +P +A F + NP G A Sbjct: 170 YLVVLSVEFKLTKGDPEDILAAMCAIRRRRELKQPIDLP----SAGSFFK---NPVGDFA 222 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 0.322 0.137 0.399 Gapped Lambda K H 0.267 0.0665 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,980,167 Number of extensions: 97951 Number of successful extensions: 265 Number of sequences better than 10.0: 1 Number of HSP's gapped: 265 Number of HSP's successfully gapped: 29 Length of query: 159 Length of database: 6,263,737 Length adjustment: 86 Effective length of query: 73 Effective length of database: 4,405,363 Effective search space: 321591499 Effective search space used: 321591499 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: 53 (24.3 bits)