RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|254780514|ref|YP_003064927.1| type II restriction endonuclease [Candidatus Liberibacter asiaticus str. psy62] (110 letters) >gnl|CDD|30495 COG0146, HyuB, N-methylhydantoinase B/acetone carboxylase, alpha subunit [Amino acid transport and metabolism / Secondary metabolites biosynthesis, transport, and catabolism]. Length = 563 Score = 27.9 bits (62), Expect = 0.73 Identities = 16/83 (19%), Positives = 28/83 (33%), Gaps = 8/83 (9%) Query: 3 FNEIILKNISNNYEVPKMLITELSTELFNLKTANQNFFHNTLTKKFGD-----YMSKITP 57 F E IL+ + N P I +L ++ + L ++G M ++ Sbjct: 161 FREDILRILLRNVRTPDYNIGDLKAQIAANLKGRRRV--RELIDEYGLDTVEEAMKEVIE 218 Query: 58 YLYEWVLSNTQSRRSRDGQEFEY 80 Y V + + EFE Sbjct: 219 YAERAVRAVIRKLPDGKY-EFED 240 >gnl|CDD|32971 COG3157, Hcp, Hemolysin-coregulated protein (uncharacterized) [Function unknown]. Length = 162 Score = 26.4 bits (58), Expect = 1.7 Identities = 13/49 (26%), Positives = 18/49 (36%), Gaps = 8/49 (16%) Query: 47 KFGDYMSKITPYLYEWVLSNTQ--------SRRSRDGQEFEYIIYSLYN 87 F + K +P LY+ S R GQ+ EY+ L N Sbjct: 62 TFTKPIDKASPLLYKACSSGETLKTAVLTWYRTGDAGQQEEYLTIKLTN 110 >gnl|CDD|143183 cd04982, IgV_TCR_gamma, Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) gamma chain. IgV_TCR_gamma: immunoglobulin (Ig) variable (V) domain of the gamma chain of gamma/delta T-cell receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are heterodimers consisting of alpha and beta chains or gamma and delta chains. Each chain contains a variable (V) and a constant (C) region. The majority of T cells contain alpha/beta TCRs but a small subset contain gamma/delta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. Gamma/delta TCRs recognize intact protein antigens; they recognize protein antigens directly and without antigen processing, and MHC independently of the bound peptide. Gamma/delta T cells can also be stimulated by non-peptide antigens such as small phosphate- or amine-containing compounds. The variable domain of gamma/delta TCRs is responsible for antigen recognition and is located at the N-terminus of the receptor. Length = 116 Score = 25.8 bits (57), Expect = 2.5 Identities = 7/30 (23%), Positives = 12/30 (40%), Gaps = 2/30 (6%) Query: 71 RSRDGQEFEYIIYSLYNINTFVTHLMHKKK 100 R + GQ E ++Y + + L K Sbjct: 36 RQKPGQALERLLY--VSSTSTQRKLSGGTK 63 >gnl|CDD|36446 KOG1232, KOG1232, KOG1232, Proteins containing the FAD binding domain [Energy production and conversion]. Length = 511 Score = 25.6 bits (56), Expect = 3.0 Identities = 17/64 (26%), Positives = 27/64 (42%), Gaps = 1/64 (1%) Query: 38 NFFHNTLTKKFGDYMSK-ITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLM 96 N N ++F + K + P++YEWV + S + G F Y Y+ + LM Sbjct: 433 NLHLNIAVREFNKEIEKLLEPFVYEWVSKHKGSISAEHGIGFLKKPYLHYSKSPEEILLM 492 Query: 97 HKKK 100 K Sbjct: 493 KDLK 496 >gnl|CDD|36455 KOG1241, KOG1241, KOG1241, Karyopherin (importin) beta 1 [Nuclear structure, Intracellular trafficking, secretion, and vesicular transport]. Length = 859 Score = 25.3 bits (55), Expect = 3.8 Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 1/29 (3%) Query: 42 NTLTKKFGDYMSKITPYLYEWVLSNTQSR 70 +L K F YM PYL LSN Q Sbjct: 626 ESLGKGFAKYMPAFKPYLLM-GLSNFQEY 653 >gnl|CDD|147760 pfam05783, DLIC, Dynein light intermediate chain (DLIC). This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo. Length = 490 Score = 25.2 bits (55), Expect = 4.0 Identities = 13/40 (32%), Positives = 19/40 (47%) Query: 38 NFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQE 77 NFF++ L+KK G S +NTQ + GQ+ Sbjct: 422 NFFNSLLSKKTGSPGSPGGGGSPAGTGTNTQGTAKKSGQK 461 >gnl|CDD|173954 cd08195, DHQS, Dehydroquinate synthase (DHQS) catalyzes the conversion of DAHP to DHQ in shikimate pathway for aromatic compounds synthesis. Dehydroquinate synthase (DHQS) catalyzes the conversion of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP) to dehydroquinate (DHQ) in the second step of the shikimate pathway. This pathway, which involves seven sequential enzymatic steps in the conversion of erythrose 4-phosphate and phosphoenolpyruvate into chorismate for subsequent synthesis of aromatic compounds, is found in bacteria, microbial eukaryotes, and plants, but not in mammals. Therefore, enzymes of this pathway are attractive targets for the development of non-toxic antimicrobial compounds, herbicides and anti-parasitic agents. The activity of DHQS requires nicotinamide adenine dinucleotide (NAD) as cofactor. A single active site in DHQS catalyzes five sequential reactions involving alcohol oxidation, phosphate elimination, carbonyl reduction, ring opening, and intramolecular aldol condensation. The binding of substrates and ligands induces domain conformational changes. In some fungi and protozoa, this domain is fused with the other four domains in shikimate pathway and forms a penta-domain AROM protein, which catalyzes steps 2-6 in the shikimate pathway. Length = 345 Score = 25.1 bits (56), Expect = 4.6 Identities = 8/25 (32%), Positives = 14/25 (56%) Query: 59 LYEWVLSNTQSRRSRDGQEFEYIIY 83 L+EW+ N ++ + D + E II Sbjct: 186 LFEWLEENKEAILALDPEALEEIIA 210 >gnl|CDD|39472 KOG4271, KOG4271, KOG4271, Rho-GTPase activating protein [Signal transduction mechanisms]. Length = 1100 Score = 24.7 bits (53), Expect = 5.4 Identities = 11/58 (18%), Positives = 20/58 (34%) Query: 43 TLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLMHKKK 100 T KF +S+ P W + + R D + + + F H+ K+ Sbjct: 53 TAKDKFETLVSQAVPLHTYWNQVSAKIDRHPDYMNYVTLEGTRKAFEMFERHISELKE 110 >gnl|CDD|37037 KOG1826, KOG1826, KOG1826, Ras GTPase activating protein RasGAP/neurofibromin [Defense mechanisms]. Length = 2724 Score = 24.2 bits (52), Expect = 8.6 Identities = 19/74 (25%), Positives = 28/74 (37%), Gaps = 9/74 (12%) Query: 3 FNEIILKNISNN-YEVPKMLITELSTELFNLKTANQNFFHNT--LTKKFGDYMSKITPYL 59 FN + LK +E P E ELF F++ ++ Y+S T L Sbjct: 1873 FNPVSLKIYFQVLHENPPHYKLEFLEELF------SGKFNSVYEISHLCLVYVSPWTGVL 1926 Query: 60 YEWVLSNTQSRRSR 73 E+ SN +R Sbjct: 1927 VEFTKSNDDEKRLI 1940 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 0.132 0.375 Gapped Lambda K H 0.267 0.0626 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 1,235,726 Number of extensions: 55506 Number of successful extensions: 144 Number of sequences better than 10.0: 1 Number of HSP's gapped: 143 Number of HSP's successfully gapped: 20 Length of query: 110 Length of database: 6,263,737 Length adjustment: 76 Effective length of query: 34 Effective length of database: 4,621,453 Effective search space: 157129402 Effective search space used: 157129402 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)