RPS-BLAST 2.2.22 [Sep-27-2009] Database: pdb70 24,244 sequences; 5,693,230 total letters Searching..................................................done Query= gi|254780763|ref|YP_003065176.1| hypothetical protein CLIBASIA_03260 [Candidatus Liberibacter asiaticus str. psy62] (107 letters) >1j8b_A YBAB; hypothetical protein, structural genomics, structure 2 function project, S2F, unknown function; HET: MSE; 1.75A {Haemophilus influenzae rd KW20} SCOP: d.222.1.1 PDB: 1pug_A Length = 112 Score = 107 bits (269), Expect = 6e-25 Identities = 45/107 (42%), Positives = 69/107 (64%), Gaps = 1/107 (0%) Query: 1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLF 60 + ++ Q +++Q KM+KM+E I LE G +G G+V + ING + + ID SL+ Sbjct: 7 KGGLGGLMKQAQQMQEKMQKMQEEIAQLEVTGESGAGLVKITINGAHNCRRIDIDPSLME 66 Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGLKFPF 107 +D E+LEDLI AA +DA ++ E+L K +T G+P+PPG+KFPF Sbjct: 67 DD-KEMLEDLIAAAFNDAVRRAEELQKEKMASVTAGMPLPPGMKFPF 112 >1ybx_A Conserved hypothetical protein; structural genomics, PSI, protein structure initiative, southeast collaboratory for structural genomics; HET: MSE; 1.80A {Clostridium thermocellum} Length = 143 Score = 103 bits (258), Expect = 1e-23 Identities = 36/101 (35%), Positives = 63/101 (62%) Query: 3 NIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFED 62 NI +V Q +++Q ME+++E + E +AGGG V+V G+ + + I ++ D Sbjct: 42 NINNLVKQAQKMQRDMERVQEELKEKTVEASAGGGAVTVVATGRKDIKEITIKPEVVDPD 101 Query: 63 NVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGL 103 +VE+L+DLI+AA ++A +K +++V + +IT GL PGL Sbjct: 102 DVEMLQDLILAAVNEALRKADEMVTAEISKITGGLGGIPGL 142 >3f42_A Protein HP0035; helicobacter pylori unknown-function, structural genomics, PSI-2, protein structure initiative; HET: MSE; 1.78A {Helicobacter pylori} Length = 99 Score = 83.2 bits (206), Expect = 1e-17 Identities = 22/97 (22%), Positives = 46/97 (47%), Gaps = 2/97 (2%) Query: 1 MSNIMKMVGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLF 60 + ++ G ++ + +++E +GGGMVSV NG L ++ID SLL Sbjct: 2 HMDFSQLGGLLDGMKKEFSQLEEKNKDTIHTSKSGGGMVSVSFNGLGELVDLQIDDSLL- 60 Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGL 97 ++ E ++ +++A +D +K +E+ + Sbjct: 61 -EDKEAMQIYLMSALNDGYKAVEENRKNLAFNMLGNF 96 >3lhp_S 4E10_D0_1ISEA_004_N (T93); epitope-scaffold, immune system; 2.70A {Artificial gene} PDB: 1y69_8 Length = 123 Score = 27.8 bits (62), Expect = 0.64 Identities = 8/36 (22%), Positives = 14/36 (38%) Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEG 96 ++ + A KKIE +A +T+G Sbjct: 88 WFDISQSLWDVQKLTDAAIKKIEAALADMEAWLTQG 123 >3hvb_A Protein FIMX; EAL phosphodiesterase, biofilm, C-DI-GMP, hydrolase; 2.99A {Pseudomonas aeruginosa PAO1} Length = 437 Score = 27.5 bits (59), Expect = 0.74 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 4/44 (9%) Query: 52 VKIDRSLLFE----DNVEILEDLIIAAHSDAHKKIEDLVATKTQ 91 +KID S + + +N EIL+ LI H I V + + Sbjct: 361 IKIDGSFVQDLNQVENQEILKGLIAELHEQQKLSIVPFVESASV 404 >2prg_C Nuclear receptor coactivator SRC-1, peroxisome proliferator activated receptor gamma; complex (thiazolidinedione/receptor), ligand-binding domain; HET: BRL; 2.30A {Homo sapiens} SCOP: j.112.1.1 Length = 88 Score = 26.8 bits (59), Expect = 1.1 Identities = 6/32 (18%), Positives = 12/32 (37%) Query: 73 AAHSDAHKKIEDLVATKTQEITEGLPIPPGLK 104 + +S K+ L+ T ++ I K Sbjct: 2 SKYSQTSHKLVQLLTTTAEQQLRHADIDTSCK 33 >1eh1_A Ribosome recycling factor; translation, hinge variability; 2.60A {Thermus thermophilus} SCOP: d.67.3.1 PDB: 2qbe_6 2qbg_6 2qbi_6* 2qbk_6* 2v46_Y* 2v48_Y* 2z4l_6* 2z4n_6* Length = 185 Score = 26.6 bits (59), Expect = 1.6 Identities = 15/82 (18%), Positives = 29/82 (35%), Gaps = 14/82 (17%) Query: 12 KEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLI 71 + ++ E+ + +I + +R + L + + L ED + E I Sbjct: 116 RAVRQYAEEGRVAIRN-------------IRREALDKLKKLAKELHLS-EDETKRAEAEI 161 Query: 72 IAAHSDAHKKIEDLVATKTQEI 93 + K + L K QEI Sbjct: 162 QKITDEFIAKADQLAEKKEQEI 183 >1c4z_A E6AP, ubiquitin-protein ligase E3A; bilobal structure, elongated shape, E3 ubiquitin ligase, E2 ubiquitin conjugating enzyme; 2.60A {Homo sapiens} SCOP: d.148.1.1 PDB: 1d5f_A Length = 358 Score = 26.2 bits (57), Expect = 1.8 Identities = 7/32 (21%), Positives = 17/32 (53%) Query: 52 VKIDRSLLFEDNVEILEDLIIAAHSDAHKKIE 83 +K+ R + +D + LE + + +D K++ Sbjct: 8 LKVRRDHIIDDALVRLEMIAMENPADLKKQLY 39 >2jae_A L-amino acid oxidase; oxidoreductase, dimerisation mode, hydride transfer mechanism, GR2-family, flavoenzyme, FAD containing; HET: FAD; 1.25A {Rhodococcus opacus} PDB: 2jb1_A* 2jb2_A* 2jb3_A* Length = 489 Score = 26.0 bits (55), Expect = 1.8 Identities = 10/62 (16%), Positives = 19/62 (30%) Query: 24 SITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSDAHKKIE 83 +T LEA GG + + R + + + E + + I Sbjct: 36 KVTVLEARTRPGGRVWTARGGSEETDLSGETQKCTFSEGHFYNVGATRIPQSHITLDYCR 95 Query: 84 DL 85 +L Sbjct: 96 EL 97 >1q1l_A Chorismate synthase; beta alpha beta sandwich, structural genomics, PSI, protein structure initiative, midwest center for structural genomics; 2.05A {Aquifex aeolicus} SCOP: d.258.1.1 Length = 401 Score = 25.6 bits (56), Expect = 2.5 Identities = 8/29 (27%), Positives = 14/29 (48%) Query: 17 KMEKMKESITSLEAEGNAGGGMVSVRING 45 K E+ K I ++ +G + GG+ V Sbjct: 209 KDEEFKTYIDEVKEKGESLGGVFEVFALN 237 >1dd5_A Ribosome recycling factor; three-helix bundle, beta-alpha-beta sandwich; 2.55A {Thermotoga maritima} SCOP: d.67.3.1 PDB: 1t1m_C Length = 185 Score = 25.7 bits (56), Expect = 2.5 Identities = 10/35 (28%), Positives = 20/35 (57%) Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITE 95 ED+ + LE+ I + +K++++ K +EI E Sbjct: 150 EDDAKRLENEIQKLTDEFIEKLDEVFEIKKEEIME 184 >3er0_A Eukaryotic translation initiation factor 5A-2; yeast, low resolution, acetylation, hypusine, phosphoprotein, protein biosynthesis; 3.35A {Saccharomyces cerevisiae} Length = 167 Score = 25.6 bits (56), Expect = 2.9 Identities = 13/59 (22%), Positives = 24/59 (40%), Gaps = 4/59 (6%) Query: 8 VGQFKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEI 66 F I+ + K+ + TS G G V + ++ TG K++ N+E+ Sbjct: 38 KNGFVVIKSRPCKIVDMSTS--KTGKHGHAKV--HLVAIDIFTGKKLEDLSPSTHNMEV 92 >1is1_A Ribosome recycling factor; translation; 2.20A {Vibrio parahaemolyticus} SCOP: d.67.3.1 Length = 185 Score = 25.6 bits (56), Expect = 3.0 Identities = 11/35 (31%), Positives = 19/35 (54%) Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITE 95 ED ++ I A KKI++++A K +E+ E Sbjct: 150 EDEDRKAQEEIQKLTDVAVKKIDEVLAAKEKELME 184 >1ise_A Ribosome recycling factor; translation; 2.20A {Escherichia coli} SCOP: d.67.3.1 PDB: 1ek8_A* 1zn0_A 1zn1_A 2rdo_8 Length = 185 Score = 25.6 bits (56), Expect = 3.3 Identities = 17/78 (21%), Positives = 34/78 (43%), Gaps = 2/78 (2%) Query: 19 EKMKESITSLEAEGN-AGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDLIIAAHSD 77 E+ K+ + E A + +V + + + + D+ + ED+ +D + Sbjct: 108 ERRKDLTKIVRGEAEQARVAVRNVGRDANDKVKALLKDKEI-SEDDDRRSQDDVQKLTDA 166 Query: 78 AHKKIEDLVATKTQEITE 95 A KKIE +A K E+ + Sbjct: 167 AIKKIEAALADKEAELMQ 184 >1wqg_A Ribosome recycling factor; translation factor, triple-helix bundle, protein synthesis; 2.15A {Mycobacterium tuberculosis} SCOP: d.67.3.1 PDB: 1wqf_A 1wqh_A Length = 185 Score = 24.9 bits (54), Expect = 4.2 Identities = 10/35 (28%), Positives = 15/35 (42%) Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITE 95 ED V E + +I++LV K E+ E Sbjct: 150 EDEVGRAEKDLDKTTHQYVTQIDELVKHKEGELLE 184 >3h7f_A Serine hydroxymethyltransferase 1; cytoplasm, one-carbon metabolism, pyridoxal phosphate, structural genomics; HET: LLP; 1.50A {Mycobacterium tuberculosis} Length = 447 Score = 25.0 bits (54), Expect = 4.4 Identities = 6/44 (13%), Positives = 15/44 (34%) Query: 61 EDNVEILEDLIIAAHSDAHKKIEDLVATKTQEITEGLPIPPGLK 104 + + D+I A + + + + P+ GL+ Sbjct: 397 DTEFTEVADIIATALATGSSVDVSALKDRATRLARAFPLYDGLE 440 >2kyy_A Possible ATP-dependent DNA helicase RECG-related; structural genomics, northeast structural genomics consortiu AAA_4 domain, PSI-2; NMR {Nitrosomonas europaea} Length = 153 Score = 24.3 bits (52), Expect = 6.6 Identities = 10/61 (16%), Positives = 23/61 (37%) Query: 11 FKEIQGKMEKMKESITSLEAEGNAGGGMVSVRINGKNMLTGVKIDRSLLFEDNVEILEDL 70 K + + E++ + E GG + + ++ G + R + D ++ DL Sbjct: 22 AKRASDMGKSVMETVIAFANEPGLDGGYLLLGVDWAINDKGDTVYRPVGLPDPDKVQRDL 81 Query: 71 I 71 Sbjct: 82 A 82 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 0.314 0.134 0.363 Gapped Lambda K H 0.267 0.0646 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 24244 Number of Hits to DB: 888,361 Number of extensions: 38288 Number of successful extensions: 153 Number of sequences better than 10.0: 1 Number of HSP's gapped: 149 Number of HSP's successfully gapped: 35 Length of query: 107 Length of database: 5,693,230 Length adjustment: 71 Effective length of query: 36 Effective length of database: 3,971,906 Effective search space: 142988616 Effective search space used: 142988616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.2 bits)