RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254781196|ref|YP_003065609.1| DNA ligase, NAD-dependent [Candidatus Liberibacter asiaticus str. psy62] (119 letters) >gnl|CDD|30621 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]. Length = 667 Score = 57.5 bits (139), Expect = 8e-10 Identities = 25/66 (37%), Positives = 34/66 (51%) Query: 53 SLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDH 112 + S EA E+E L ++ H YY LD P +D YD++ L L+E+ PEL D Sbjct: 1 AWSMAEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQELEEKHPELITPDS 60 Query: 113 PWNTVG 118 P VG Sbjct: 61 PTQRVG 66 >gnl|CDD|145016 pfam01653, DNA_ligase_aden, NAD-dependent DNA ligase adenylation domain. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilising either ATP or NAD(+) as a cofactor. This domain is the catalytic adenylation domain. The NAD+ group is covalently attached to this domain at the lysine in the KXDG motif of this domain. This enzyme- adenylate intermediate is an important feature of the proposed catalytic mechanism. Length = 315 Score = 54.2 bits (131), Expect = 8e-09 Identities = 27/61 (44%), Positives = 34/61 (55%) Query: 58 EAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTV 117 EA E+ L ++ + YY LDNP D YDR+ RL AL+E+FPEL D P V Sbjct: 2 EAQQEIARLRELIRQYDYHYYVLDNPEVPDAEYDRLYRRLQALEEKFPELITPDSPTQRV 61 Query: 118 G 118 G Sbjct: 62 G 62 >gnl|CDD|29013 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.. Length = 307 Score = 52.1 bits (125), Expect = 4e-08 Identities = 22/57 (38%), Positives = 29/57 (50%) Query: 62 EVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELFDEDHPWNTVG 118 + L ++ H YY LD P +D YDR+ L AL+E+ PEL D P VG Sbjct: 2 RIAELRELLNKHDYRYYVLDEPSVSDAEYDRLYRELRALEEEHPELKTPDSPTQRVG 58 >gnl|CDD|144194 pfam00508, PPV_E2_N, E2 (early) protein, N terminal. Length = 201 Score = 27.8 bits (63), Expect = 0.76 Identities = 13/18 (72%), Positives = 16/18 (88%) Query: 94 SERLDALQEQFPELFDED 111 SERLDALQEQ EL+++D Sbjct: 4 SERLDALQEQLLELYEKD 21 >gnl|CDD|63853 cd04384, RhoGAP_CdGAP, RhoGAP_CdGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of CdGAP-like proteins; CdGAP contains an N-terminal RhoGAP domain and a C-terminal proline-rich region, and it is active on both Cdc42 and Rac1 but not RhoA. CdGAP is recruited to focal adhesions via the interaction with the scaffold protein actopaxin (alpha-parvin). 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 = 195 Score = 26.5 bits (58), Expect = 2.0 Identities = 13/26 (50%), Positives = 17/26 (65%), Gaps = 1/26 (3%) Query: 75 KWYYR-LDNPLFTDGLYDRVSERLDA 99 K Y+R L NPL T LY++ SE + A Sbjct: 80 KLYFRELPNPLLTYQLYEKFSEAVSA 105 >gnl|CDD|143504 cd06831, PLPDE_III_ODC_like_AZI, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Ornithine Decarboxylase-like Antizyme Inhibitor. Antizyme inhibitor (AZI) is homologous to the fold type III PLP-dependent enzyme ODC but does not retain any decarboxylase activity. Like ODC, AZI is presumed to exist as a homodimer. Antizyme is a regulatory protein that binds directly to the ODC monomer to block its active site, leading to its degradation by the 26S proteasome. AZI binds to Antizyme with a higher affinity than ODC, preventing the formation of the Antizyme-ODC complex. Thus, AZI blocks the ability of Antizyme to promote ODC degradation, which leads to increased ODC enzymatic activity and polyamine levels. AZI also prevents the degradation of other proteins regulated by Antizyme, such as cyclin D1. Length = 394 Score = 26.0 bits (57), Expect = 2.5 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 4/37 (10%) Query: 73 HQKWYYRLDNPLFTDGLYDRVSERLDALQEQ--FPEL 107 H+K Y+ D PLFT L+ + LD + E PEL Sbjct: 314 HKK--YKEDEPLFTSSLWGPSCDELDQIVESCLLPEL 348 >gnl|CDD|37310 KOG2099, KOG2099, KOG2099, Glycogen phosphorylase [Carbohydrate transport and metabolism]. Length = 843 Score = 26.1 bits (57), Expect = 2.7 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%) Query: 8 FRSSKFENEHN-ITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSK 56 KF+N+ N ITP +W L L ++ E W+ ++T L K Sbjct: 476 LEPEKFQNKTNGITPRRWLLLCNPGLADLITEKIGEEWITDLDQLTKLRK 525 >gnl|CDD|33492 COG3696, COG3696, Putative silver efflux pump [Inorganic ion transport and metabolism]. Length = 1027 Score = 25.6 bits (56), Expect = 3.0 Identities = 14/28 (50%), Positives = 16/28 (57%), Gaps = 5/28 (17%) Query: 84 LFTDG--LY---DRVSERLDALQEQFPE 106 +F DG LY RV ERL +Q Q PE Sbjct: 96 IFKDGTDLYWARQRVLERLSQVQSQLPE 123 >gnl|CDD|145808 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain. Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Length = 297 Score = 25.7 bits (57), Expect = 3.3 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%) Query: 12 KFENEHNITPAQWKKLLTLEAKFLPNKRALESWLDKAKKVTSLSKGEAMIEVE 64 K E ++N P + K + +FL +K A+E + + + +L+ E IE E Sbjct: 159 KLEAKYNQVPRKGVKAEEVLQEFLNSKEAVEEAILQTDQ--ALTAKEKAIEAE 209 >gnl|CDD|35731 KOG0511, KOG0511, KOG0511, Ankyrin repeat protein [General function prediction only]. Length = 516 Score = 25.4 bits (55), Expect = 4.2 Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 1/39 (2%) Query: 4 FDRVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALE 42 F + + N + Q+ LL++E KF K +LE Sbjct: 200 FSPFLKQ-LYLNTNAEWKDQYNALLSIEVKFSKEKLSLE 237 >gnl|CDD|143492 cd06818, PLPDE_III_cryptic_DSD, Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme Bacterial Cryptic D-Serine Dehydratase. This subfamily is composed of Burkholderia cepacia cryptic D-serine dehydratase (cryptic DSD), which is also called D-serine deaminase, and similar bacterial proteins. Members of this subfamily are fold type III PLP-dependent enzymes with similarity to bacterial alanine racemase (AR), which contains an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as dimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. Based on similarity, it is possible cryptic DSDs may also form dimers. Cryptic DSDs are distinct from the ubiquitous bacterial DSDs coded by the dsdA gene, mammalian L-serine dehydratases (LSD) and mammalian serine racemase (SerRac), which are fold type II PLP-dependent enzymes. At present, the enzymatic and biochemical properties of cryptic DSDs are still poorly understood. Typically, DSDs catalyze the dehydration of D-serine to aminoacrylate, which is rapidly hydrolyzed to pyruvate and ammonia. Length = 382 Score = 24.9 bits (55), Expect = 5.4 Identities = 9/32 (28%), Positives = 13/32 (40%), Gaps = 3/32 (9%) Query: 77 YYRLDNPLFTDG---LYDRVSERLDALQEQFP 105 + + T G +D V+E L AL P Sbjct: 202 LFPDRELILTAGGSAWFDLVAEALAALALDGP 233 >gnl|CDD|38151 KOG2940, KOG2940, KOG2940, Predicted methyltransferase [General function prediction only]. Length = 325 Score = 24.2 bits (52), Expect = 9.2 Identities = 12/61 (19%), Positives = 26/61 (42%) Query: 49 KKVTSLSKGEAMIEVEYLVKIALHHQKWYYRLDNPLFTDGLYDRVSERLDALQEQFPELF 108 ++ ++ + I L +I W N + + DR+++R+ ++ FP F Sbjct: 18 ASLSFSTESKVKIFDRDLKRIQRDRAAWLSDQKNDYLKEEIGDRLADRVFDCKKSFPTAF 77 Query: 109 D 109 D Sbjct: 78 D 78 >gnl|CDD|176897 cd08888, SRPBCC_PITPNA-B_like, Lipid-binding SRPBCC domain of mammalian PITPNA, -B, and related proteins (Class I PITPs). This subgroup includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of mammalian Class 1 phosphatidylinositol transfer proteins (PITPs), PITPNA/PITPalpha and PITPNB/PITPbeta, Drosophila vibrator, and related proteins. These are single domain proteins belonging to the PITP family of lipid transfer proteins, and to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. In vitro, PITPs bind phosphatidylinositol (PtdIns), as well as phosphatidylcholine (PtdCho) but with a lower affinity. They transfer these lipids from one membrane compartment to another. The cellular roles of PITPs include inositol lipid signaling, PtdIns metabolism, and membrane trafficking. In addition, PITPNB transfers sphingomyelin in vitro, with a low affinity. PITPNA is found chiefly in the nucleus and cytoplasm; it is enriched in the brain and predominantly localized in the axons. A reduced expression of PITPNA contributes to the neurodegenerative phenotype of the mouse vibrator mutation. The role of PITPNA in vivo may be to provide PtdIns for localized PI3K-dependent signaling, thereby controlling the polarized extension of axonal processes. PITPNA homozygous null mice die soon after birth from complicated organ failure, including intestinal and hepatic steatosis, hypoglycemia, and spinocerebellar disease. PITPNB is associated with the Golgi and ER, and is highly expressed in the liver. Deletion of the PITPNB gene results in embryonic lethality. The PtdIns and PtdCho exchange activity of PITPNB is required for COPI-mediated retrograde transport from the Golgi to the ER. Drosophila vibrator localizes to the ER, and has an essential role in cytokinesis during mitosis and meiosis. Length = 258 Score = 24.3 bits (53), Expect = 9.2 Identities = 7/15 (46%), Positives = 10/15 (66%) Query: 12 KFENEHNITPAQWKK 26 EN HN+ P +WK+ Sbjct: 120 TQENVHNLDPEEWKE 134 >gnl|CDD|37255 KOG2044, KOG2044, KOG2044, 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair, RNA processing and modification]. Length = 931 Score = 24.2 bits (52), Expect = 9.5 Identities = 12/39 (30%), Positives = 19/39 (48%) Query: 6 RVFRSSKFENEHNITPAQWKKLLTLEAKFLPNKRALESW 44 R FR++K E + ++ E KFLP K E++ Sbjct: 117 RRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETF 155 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 0.319 0.135 0.419 Gapped Lambda K H 0.267 0.0636 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,539,315 Number of extensions: 71512 Number of successful extensions: 266 Number of sequences better than 10.0: 1 Number of HSP's gapped: 266 Number of HSP's successfully gapped: 32 Length of query: 119 Length of database: 6,263,737 Length adjustment: 81 Effective length of query: 38 Effective length of database: 4,513,408 Effective search space: 171509504 Effective search space used: 171509504 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 (23.6 bits)