RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

Searching..................................................done

Query= gi|254780225|ref|YP_003064638.1| peptidyl-tRNA hydrolase
[Candidatus Liberibacter asiaticus str. psy62]
         (189 letters)



>1ryb_A CRS2; alpha-beta, hydrolase; 1.70A {Zea mays} (A:)
          Length = 205

 Score =  205 bits (524), Expect = 2e-54
 Identities = 57/186 (30%), Positives = 98/186 (52%), Gaps = 3/186 (1%)

Query: 1   MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIK 60
            +++AGLGNPG++Y   RHN+GF  +DRI +         +  + +  G +  +  +++K
Sbjct: 17  PWLIAGLGNPGNKYYGTRHNVGFEMVDRIAAEEGITMNTIQSKSLLGIGSIGEVPVLVVK 76

Query: 61  PQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSISE 120
           PQ++MN SG+++  +  +Y++  L + L+I+DD  L  G LRL+  GG   HNGL+++ E
Sbjct: 77  PQSYMNYSGEAIGPLAAYYQV-PLRHILLIYDDTSLPNGVLRLQKKGGHGRHNGLQNVIE 135

Query: 121 KCG--KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDV 178
                + + RL IGIG PP        +L  FSS ER  +   ++    ++  L  +   
Sbjct: 136 HLDGRREFPRLSIGIGSPPGKMDPRAFLLQKFSSEERVQIDTALEQGVDAVRTLVLKGFS 195

Query: 179 SFLNHI 184
                 
Sbjct: 196 GSTERF 201


>2z2i_A PTH, peptidyl-tRNA hydrolase; protein synthesis; 1.98A
           {Mycobacterium tuberculosis H37RV} PDB: 2z2j_A 2z2k_A
           2jrc_A (A:)
          Length = 191

 Score =  203 bits (519), Expect = 9e-54
 Identities = 73/186 (39%), Positives = 106/186 (56%), Gaps = 3/186 (1%)

Query: 1   MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFPAWK-KKFHAEISEGQLDGLRTILI 59
             +V GLGNPG  Y   RHN+GF+  D + +         K+  AE++ G+  G   +L 
Sbjct: 4   PLLVVGLGNPGANYARTRHNLGFVVADLLAARLGAKFKAHKRSGAEVATGRSAGRSLVLA 63

Query: 60  KPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSIS 119
           KP+ +MN SG+ +  +  FY +    N +VIHDDLDL+FG +RLK GGG+ GHNGL+S+ 
Sbjct: 64  KPRCYMNESGRQIGPLAKFYSVA-PANIIVIHDDLDLEFGRIRLKIGGGEGGHNGLRSVV 122

Query: 120 EKCG-KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKREDV 178
              G K+++R+RIGIGRPP        VL NF+  ER  +  I +  A +  LL ++   
Sbjct: 123 AALGTKDFQRVRIGIGRPPGRKDPAAFVLENFTPAERAEVPTICEQAADATELLIEQGME 182

Query: 179 SFLNHI 184
              N +
Sbjct: 183 PAQNRV 188


>2pth_A Peptidyl-tRNA hydrolase; 1.20A {Escherichia coli K12} (A:)
          Length = 193

 Score =  200 bits (510), Expect = 1e-52
 Identities = 69/192 (35%), Positives = 96/192 (50%), Gaps = 4/192 (2%)

Query: 1   MFIVAGLGNPGHEYCENRHNIGFMCIDRIHSFHFFP-AWKKKFHAEISEGQLDGLRTILI 59
           + ++ GL NPG EY   RHN G   +D +      P   + KF    S   L G    L+
Sbjct: 2   IKLIVGLANPGAEYAATRHNAGAWFVDLLAERLRAPLREEAKFFGYTSRVTLGGEDVRLL 61

Query: 60  KPQTFMNLSGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGGDAGHNGLKSIS 119
            P TFMNLSG+++  + +F+++ N +  LV HD+LDL  G  + K GGG  GHNGLK I 
Sbjct: 62  VPTTFMNLSGKAVAAMASFFRI-NPDEILVAHDELDLPPGVAKFKLGGGHGGHNGLKDII 120

Query: 120 EKCG--KNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLLAKRED 177
            K G   N+ RLRIGIG P D   ++  VLG     E+  +   ID  AR   +      
Sbjct: 121 SKLGNNPNFHRLRIGIGHPGDKNKVVGFVLGKPPVSEQKLIDEAIDEAARCTEMWFTDGL 180

Query: 178 VSFLNHIVSVRK 189
               N + + + 
Sbjct: 181 TKATNRLHAFKA 192


>2cjq_A RNA-directed RNA polymerase; transferase, RNA-dependent RNA
           polymerase, nucleotidyltransferase, BVDV, helicase,
           membrane, protease; 2.60A {Bovine viral diarrhea virus}
           PDB: 1s48_A 1s49_A* 1s4f_A
           (A:128-154,A:519-598,A:664-720)
          Length = 164

 Score = 27.6 bits (61), Expect = 1.1
 Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 10/50 (20%)

Query: 123 GKNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFLLPIIDNIARSLPLL 172
           GK+Y++L++     P                ERY L PI++ + R L +L
Sbjct: 116 GKHYEQLQLQARTSP----------VTGVGTERYKLGPIVNLLLRRLRVL 155


>2vvf_A Major capsid protein P2; double jelly-roll viral capsid,
           viral protein; 2.5A {Pseudoalteromonas phage PM2} PDB:
           2w0c_A (A:1-139)
          Length = 139

 Score = 26.7 bits (59), Expect = 2.1
 Identities = 5/54 (9%), Positives = 13/54 (24%), Gaps = 7/54 (12%)

Query: 56  TILIKPQTFMNL-SGQSLLEVMNFYKLPNLENYLVIHDDLDLDFGTLRLKTGGG 108
            + +  +      +   L+     +K       +  H      F    +K    
Sbjct: 48  RVELDGRLLSTYKTLNDLILENTRHKRKIKAGVVSFH------FVRPEMKGVNV 95


>3bz5_A Internalin-J, INLJ; leucine rich repeat (LRR), cysteine
          ladder, asparagine ladder, virulence factor, solenoid,
          cell WALL; 2.70A {Listeria monocytogenes} (A:)
          Length = 457

 Score = 26.1 bits (55), Expect = 2.9
 Identities = 2/20 (10%), Positives = 5/20 (25%)

Query: 66 NLSGQSLLEVMNFYKLPNLE 85
           L         +++   N  
Sbjct: 2  TLKAGQTQSFNDWFPDDNFA 21


>3g02_A Epoxide hydrolase; alpha/beta hydrolase fold,
          enantioselective, mutant, directed evolution; 1.50A
          {Aspergillus niger} PDB: 1qo7_A 3g0i_A*
          (A:1-73,A:225-322)
          Length = 171

 Score = 25.2 bits (55), Expect = 5.5
 Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 4/32 (12%)

Query: 40 KKFHAEISEGQLDGLRTIL----IKPQTFMNL 67
            F   I + QLD L+T++    I P T+ +L
Sbjct: 18 NPFTVSIPDEQLDDLKTLVRLSKIAPPTYESL 49


>3a3d_A PBP4, penicillin-binding protein 4; DACB, hydrolase; 1.60A
           {Haemophilus influenzae} PDB: 3a3e_A* 3a3f_A* 3a3i_A*
           (A:1-43,A:331-453)
          Length = 166

 Score = 25.3 bits (55), Expect = 5.8
 Identities = 7/71 (9%), Positives = 12/71 (16%), Gaps = 16/71 (22%)

Query: 99  GTLRLKTGGGDAGHNGLKSISEKCGKNYKRLRIGIGRPPDTAHIIRHVLGNFSSPERYFL 158
             +  KTG     +N                  G         +      N  S      
Sbjct: 102 KNVIAKTGSLKGVYN----------------LAGFMTNARGEKVAFVQFINGYSTGDLES 145

Query: 159 LPIIDNIARSL 169
                 + +  
Sbjct: 146 KTKRAPLVQFE 156


>1wwl_A Monocyte differentiation antigen CD14; LPS, immune system;
           HET: NAG; 2.50A {Mus musculus} (A:)
          Length = 312

 Score = 25.2 bits (53), Expect = 6.0
 Identities = 8/74 (10%), Positives = 20/74 (27%)

Query: 12  HEYCENRHNIGFMCIDRIHSFHFFPAWKKKFHAEISEGQLDGLRTILIKPQTFMNLSGQS 71
                   ++    +             +     +S   L  +   L    + ++LS   
Sbjct: 226 ARVQLQGLDLSHNSLRDAAGAPSCDWPSQLNSLNLSFTGLKQVPKGLPAKLSVLDLSYNR 285

Query: 72  LLEVMNFYKLPNLE 85
           L    +  +LP + 
Sbjct: 286 LDRNPSPDELPQVG 299


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.325    0.144    0.445 

Gapped
Lambda     K      H
   0.267   0.0637    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 1,532,976
Number of extensions: 69734
Number of successful extensions: 172
Number of sequences better than 10.0: 1
Number of HSP's gapped: 163
Number of HSP's successfully gapped: 13
Length of query: 189
Length of database: 4,956,049
Length adjustment: 84
Effective length of query: 105
Effective length of database: 2,116,429
Effective search space: 222225045
Effective search space used: 222225045
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.0 bits)