RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254781090|ref|YP_003065503.1| hypothetical protein CLIBASIA_04960 [Candidatus Liberibacter asiaticus str. psy62] (71 letters) >1i6a_A OXYR, hydrogen peroxide-inducible genes activator; OXYR regulatory domain, oxidized form, transcription; 2.30A {Escherichia coli} SCOP: c.94.1.1 PDB: 1i69_A Length = 219 Score = 28.8 bits (63), Expect = 0.35 Identities = 4/24 (16%), Positives = 10/24 (41%) Query: 48 LADFIKDYPDCDLELENLVTDDIL 71 + + +P ++ L T +L Sbjct: 24 IPMLHQTFPKLEMYLHEAQTHQLL 47 >3geb_A EYES absent homolog 2; hydrolase, activator, alternative splicing, cytoplasm, developmental protein, magnesium, nucleus, polymorphism; 2.40A {Homo sapiens} Length = 274 Score = 28.6 bits (64), Expect = 0.36 Identities = 21/62 (33%), Positives = 31/62 (50%), Gaps = 6/62 (9%) Query: 13 VNFRFLLDGYRSGKTSKDKYQKIVKIGDHAES-IKTLAD---FIKDYPDCD-LELENLVT 67 + F LL G + + KD V+IG E I LAD F D DCD + ++++ + Sbjct: 16 IIFHSLLTGTFASRYGKD-TTTSVRIGLMMEEMIFNLADTHLFFNDLEDCDQIHVDDVSS 74 Query: 68 DD 69 DD Sbjct: 75 DD 76 >3ho7_A OXYR; beta-alpha-barrels, DNA-binding, transcription, transcriptio regulation; 1.58A {Porphyromonas gingivalis} Length = 232 Score = 27.4 bits (60), Expect = 0.91 Identities = 3/24 (12%), Positives = 9/24 (37%) Query: 48 LADFIKDYPDCDLELENLVTDDIL 71 + K+ ++ + + T L Sbjct: 30 FPIWKKELAGLEIHVSEMQTSRCL 53 >3hsq_A Acyl-[acyl-carrier-protein]--UDP-N- acetylglucosamine O-acyltransferase; L.interrogans LPXA, LPXA, LPXA acyltransferase; 2.10A {Leptospira interrogans} PDB: 3i3a_A* 3i3x_A* Length = 259 Score = 26.9 bits (58), Expect = 1.2 Identities = 8/33 (24%), Positives = 17/33 (51%) Query: 22 YRSGKTSKDKYQKIVKIGDHAESIKTLADFIKD 54 Y SG +++ ++ G+ E +K + F +D Sbjct: 218 YHSGISTRKALDELEASGNLIEQVKYIIKFFRD 250 >2xev_A YBGF; tetratricopeptide, alpha-helical, metal binding; 1.57A {Xanthomonas campestris} Length = 129 Score = 26.7 bits (59), Expect = 1.3 Identities = 6/21 (28%), Positives = 9/21 (42%) Query: 37 KIGDHAESIKTLADFIKDYPD 57 G + E+ +TL YP Sbjct: 88 GEGKNTEAQQTLQQVATQYPG 108 Score = 24.4 bits (53), Expect = 6.5 Identities = 6/32 (18%), Positives = 14/32 (43%), Gaps = 3/32 (9%) Query: 29 KDKYQKIV---KIGDHAESIKTLADFIKDYPD 57 + Y K G + ++ + F++ YP+ Sbjct: 3 RTAYNVAFDALKNGKYDDASQLFLSFLELYPN 34 >3jv9_A OXYR, transcriptional regulator, LYSR family; LYSR-type transcriptional regulator, LTTR, redox, structural genomics, OPPF; 2.39A {Neisseria meningitidis} Length = 219 Score = 26.2 bits (57), Expect = 2.1 Identities = 5/24 (20%), Positives = 8/24 (33%) Query: 48 LADFIKDYPDCDLELENLVTDDIL 71 + + P L LE T + Sbjct: 23 IVSLRRTAPKMPLMLEENYTHTLT 46 >3kos_A HTH-type transcriptional activator AMPR; alpha-beta sandwich, DNA-binding, transcription regulation; HET: MES; 1.83A {Citrobacter freundii} PDB: 3kot_A Length = 219 Score = 25.4 bits (55), Expect = 2.9 Identities = 7/17 (41%), Positives = 10/17 (58%) Query: 48 LADFIKDYPDCDLELEN 64 L+DF + YP DL + Sbjct: 31 LSDFKRSYPHIDLHIST 47 >3op5_A Serine/threonine-protein kinase VRK1; adenosine triphosphate, amino acid sequence, binding sites, domain, models, molecular; HET: REB; 2.40A {Homo sapiens} Length = 364 Score = 25.3 bits (55), Expect = 3.7 Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 3/58 (5%) Query: 11 WGVNFRFLLDGYR--SGKTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCDLELENLV 66 G L G+ KY + KI + E+I +L D + E+ + Sbjct: 247 LGYCMIQWLTGHLPWEDNLKDPKYVRDSKIR-YRENIASLMDKCFPAANAPGEIAKYM 303 >2qia_A UDP-N-acetylglucosamine acyltransferase; LEFT-handed parallel beta helix; HET: U20; 1.74A {Escherichia coli K12} SCOP: b.81.1.1 PDB: 1lxa_A 2jf3_A* 2aq9_A* 2qiv_X* 2jf2_A Length = 262 Score = 24.4 bits (52), Expect = 6.1 Identities = 10/33 (30%), Positives = 16/33 (48%) Query: 22 YRSGKTSKDKYQKIVKIGDHAESIKTLADFIKD 54 YRSGKT + +I ++ + +K DF Sbjct: 223 YRSGKTLDEVKPEIAELAETYPEVKAFTDFFAR 255 >2ckc_A Chromodomain-helicase-DNA-binding protein 7; protein-protein interaction, phosphorylation, disease mutation, nucleotide-binding; NMR {Homo sapiens} SCOP: d.76.2.1 PDB: 2v0e_A Length = 80 Score = 24.4 bits (53), Expect = 6.6 Identities = 6/19 (31%), Positives = 11/19 (57%) Query: 39 GDHAESIKTLADFIKDYPD 57 G+ A K L +++K +P Sbjct: 40 GEDAPKNKDLVEWLKLHPT 58 >3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB, transcription factor, DNA-binding, DNA-directed RNA polymerase; 4.30A {Saccharomyces cerevisiae} Length = 197 Score = 24.1 bits (52), Expect = 7.0 Identities = 3/14 (21%), Positives = 6/14 (42%) Query: 56 PDCDLELENLVTDD 69 P+C + +V Sbjct: 25 PECKVYPPKIVERF 38 >3c8f_A Pyruvate formate-lyase 1-activating enzyme; adoMet radical, SAM radical, activase, glycyl radical, 4Fe- 4S, carbohydrate metabolism, cytoplasm; HET: MT2 PGE; 2.25A {Escherichia coli} PDB: 3cb8_A* Length = 245 Score = 24.2 bits (51), Expect = 7.2 Identities = 6/34 (17%), Positives = 13/34 (38%) Query: 26 KTSKDKYQKIVKIGDHAESIKTLADFIKDYPDCD 59 +Y + D +S L +F +D + + Sbjct: 161 VKVWIRYVVVPGWSDDDDSAHRLGEFTRDMGNVE 194 >2dl6_A Chromodomain-helicase-DNA-binding protein 8; BRK, CHD8, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: d.76.2.1 Length = 83 Score = 24.1 bits (52), Expect = 8.5 Identities = 4/19 (21%), Positives = 10/19 (52%) Query: 39 GDHAESIKTLADFIKDYPD 57 G+ A L +++ +P+ Sbjct: 33 GEDAPRRAELEMWLQGHPE 51 >1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant photosynthetic reaction center, peripheral antenna; HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1 Length = 154 Score = 23.8 bits (50), Expect = 9.3 Identities = 6/17 (35%), Positives = 10/17 (58%), Gaps = 1/17 (5%) Query: 43 ESIKTLADFIKDYPDCD 59 +++K L +K Y D D Sbjct: 20 QALKKLQASLKLYAD-D 35 >2cka_A Chromodomain-helicase-DNA-binding protein 8; BRK domain, transcription elongation, chromatin remodeling, protein-protein interaction, transcription; NMR {Homo sapiens} SCOP: d.76.2.1 Length = 95 Score = 23.7 bits (51), Expect = 9.8 Identities = 4/19 (21%), Positives = 10/19 (52%) Query: 39 GDHAESIKTLADFIKDYPD 57 G+ A L +++ +P+ Sbjct: 59 GEDAPRRAELEMWLQGHPE 77 Database: pdb70 Posted date: Jan 26, 2011 11:21 AM Number of letters in database: 5,693,230 Number of sequences in database: 24,244 Lambda K H 0.321 0.144 0.434 Gapped Lambda K H 0.267 0.0573 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 653,255 Number of extensions: 23888 Number of successful extensions: 148 Number of sequences better than 10.0: 1 Number of HSP's gapped: 148 Number of HSP's successfully gapped: 25 Length of query: 71 Length of database: 5,693,230 Length adjustment: 41 Effective length of query: 30 Effective length of database: 4,699,226 Effective search space: 140976780 Effective search space used: 140976780 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: 50 (23.4 bits)