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)