RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780514|ref|YP_003064927.1| type II restriction
endonuclease [Candidatus Liberibacter asiaticus str. psy62]
         (110 letters)



>2gb7_A R.ECL18KI; ECL18KI-DNA complex, type II restriction endonuclease,
           nucleotide flipping, base extrusion, hydrolase/DNA
           complex; HET: DNA; 1.70A {Enterobacter cloacae} PDB:
           2fqz_A*
          Length = 305

 Score = 37.3 bits (86), Expect = 8e-04
 Identities = 18/40 (45%), Positives = 25/40 (62%)

Query: 48  FGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYN 87
             D+  +   ++Y+  LSNTQSRRSR G+EFE I+  L  
Sbjct: 94  IRDFTMEYPTHIYDLALSNTQSRRSRAGKEFESILELLMM 133


>1na6_A Ecorii, restriction endonuclease ecorii; site-specific restriction,
           mutation, replication, hydrolase; 2.10A {Escherichia
           coli} SCOP: b.142.1.1 c.52.1.22 PDB: 3hqg_A 3hqf_A
          Length = 404

 Score = 35.2 bits (81), Expect = 0.003
 Identities = 7/24 (29%), Positives = 12/24 (50%)

Query: 64  LSNTQSRRSRDGQEFEYIIYSLYN 87
            S +  R+SR G+  E  +  L+ 
Sbjct: 256 NSVSNRRKSRAGKSLELHLEHLFI 279


>3bm3_A PSPGI restriction endonuclease; endonuclease-DNA complex,
           restriction enzyme, PSPGI, base flipping, hydrolase/DNA
           complex; HET: DNA MSE CIT; 1.70A {Pyrococcus SP}
          Length = 272

 Score = 33.5 bits (76), Expect = 0.011
 Identities = 13/39 (33%), Positives = 17/39 (43%), Gaps = 1/39 (2%)

Query: 49  GDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYN 87
             Y+S       +   S  Q+R SR G+ FE I   L N
Sbjct: 76  EAYLSAGYSR-EKLEQSFQQARFSRGGKAFEIIFTKLLN 113


>1ho8_A Vacuolar ATP synthase subunit H; heat repeat, hydrolase; 2.95A
           {Saccharomyces cerevisiae} SCOP: a.118.1.9
          Length = 480

 Score = 25.4 bits (55), Expect = 3.2
 Identities = 18/79 (22%), Positives = 29/79 (36%), Gaps = 5/79 (6%)

Query: 37  QNFFHNTLTKKFGDYMSKITPYLYEWVLSNTQSRRSRDGQEFEYIIYSLYNINTFVTHLM 96
            N F +    +F     KI   L E + +  ++      QE   I  +L +I   V  L 
Sbjct: 378 DNGFWSDNIDEFKKDNYKIFRQLIELLQAKVRNGDVNAKQEKIIIQVALNDITHVVELLP 437

Query: 97  H-----KKKSGKALSLSIM 110
                  K  GKA  + ++
Sbjct: 438 ESIDVLDKTGGKADIMELL 456


>1dlf_L Anti-dansyl immunoglobulin IGG2A(S); FV fragment; 1.45A {Mus
           musculus} SCOP: b.1.1.1 PDB: 1wz1_L* 2dlf_L 1maj_A
           1mak_A 1ktr_L 2cju_L* 2uud_K* 1dsf_L 1n4x_L 1bfv_L*
           1cfv_L* 2bfv_L* 1wt5_C
          Length = 113

 Score = 23.8 bits (51), Expect = 8.4
 Identities = 10/39 (25%), Positives = 16/39 (41%)

Query: 71  RSRDGQEFEYIIYSLYNINTFVTHLMHKKKSGKALSLSI 109
             + GQ  + +IY + N  + V        SG   +L I
Sbjct: 42  LQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKI 80


>3he1_A Major exported HCP3 protein; structural genomics, APC22128, HCPC,
           secretion, virulence, PSI-2, protein structure
           initiative; 2.10A {Pseudomonas aeruginosa}
          Length = 195

 Score = 24.1 bits (52), Expect = 8.8
 Identities = 10/67 (14%), Positives = 17/67 (25%), Gaps = 13/67 (19%)

Query: 34  TANQNFFHNTLTKKFGD-----YMSKITPYLYEWVLSNTQ--------SRRSRDGQEFEY 80
             +      T  +            K +P L   + S  +         R S  G +  Y
Sbjct: 73  PRDPQSGQPTGQRVHKPVVITKVFDKASPLLLAALTSGERLTKVEIQWYRTSAAGTQEHY 132

Query: 81  IIYSLYN 87
               L +
Sbjct: 133 YTTVLED 139


  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
   0.319    0.132    0.375 

Gapped
Lambda     K      H
   0.267   0.0602    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 869,931
Number of extensions: 33127
Number of successful extensions: 96
Number of sequences better than 10.0: 1
Number of HSP's gapped: 96
Number of HSP's successfully gapped: 15
Length of query: 110
Length of database: 5,693,230
Length adjustment: 74
Effective length of query: 36
Effective length of database: 3,899,174
Effective search space: 140370264
Effective search space used: 140370264
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 (23.3 bits)