RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy11111
         (84 letters)



>1gqi_A Alpha-glucuronidase; (alpha-beta)8 barrel, glycoside hydrolase;
           1.48A {Pseudomonas cellulosa} SCOP: c.1.8.10 d.92.2.2
           PDB: 1gqj_A* 1gqk_A* 1gql_A* 1h41_A*
          Length = 708

 Score = 26.8 bits (59), Expect = 0.80
 Identities = 10/36 (27%), Positives = 15/36 (41%), Gaps = 5/36 (13%)

Query: 17  PQDYCWRHSSIGTAYASLLSPYGGTQQLSNIMVKTF 52
           PQ Y   H+      A+ L P+GG      +  + F
Sbjct: 293 PQGYGRDHAEGANMLAAALKPFGGV-----VFWRAF 323


>3h93_A Thiol:disulfide interchange protein DSBA; disulfide bond,
          redox-active center, transcription regulator; HET: MSE
          GOL; 1.50A {Pseudomonas aeruginosa PAO1}
          Length = 192

 Score = 25.5 bits (55), Expect = 2.2
 Identities = 15/57 (26%), Positives = 20/57 (35%), Gaps = 9/57 (15%)

Query: 28 GTAYASLLSPYGGTQQLSNIMVKTFQAYLPNCHRTYSCVHCRAHLASHDELISKIPR 84
          G  Y  L SP   +Q     +V+ F          Y C HC A   +      K+P 
Sbjct: 9  GKEYVELSSPVPVSQPGKIEVVELF---------WYGCPHCYAFEPTIVPWSEKLPA 56


>3r44_A Fatty acyl COA synthetase FADD13 (fatty-acyl-COA synthetase);
           ligase; HET: HIS; 1.80A {Mycobacterium tuberculosis}
           PDB: 3t5c_A 3t5b_A
          Length = 517

 Score = 25.2 bits (56), Expect = 2.5
 Identities = 5/18 (27%), Positives = 9/18 (50%), Gaps = 5/18 (27%)

Query: 67  HCRAHLASHDELISKIPR 84
           +C   LA +     K+P+
Sbjct: 474 YCGTRLARY-----KLPK 486


>3ipl_A 2-succinylbenzoate--COA ligase; structural genomics, acyl-protein
           synthetase, PSI-2, protein structure initiative; 2.30A
           {Staphylococcus aureus subsp}
          Length = 501

 Score = 24.8 bits (55), Expect = 3.4
 Identities = 5/18 (27%), Positives = 9/18 (50%), Gaps = 5/18 (27%)

Query: 67  HCRAHLASHDELISKIPR 84
           +   HLA +     K+P+
Sbjct: 458 YLSKHLAKY-----KVPK 470


>3nyq_A Malonyl-COA ligase; A/B topology ababa sandwich beta-barrel
           adenylate-forming EN fold; HET: MCA AMP; 1.43A
           {Streptomyces coelicolor} PDB: 3nyr_A*
          Length = 505

 Score = 24.9 bits (55), Expect = 3.7
 Identities = 8/18 (44%), Positives = 8/18 (44%), Gaps = 5/18 (27%)

Query: 67  HCRAHLASHDELISKIPR 84
           H  A LA H     K PR
Sbjct: 469 HVAARLAPH-----KRPR 481


>3ky9_A Proto-oncogene VAV; calponin homology domain, DBL homology domain,
           pleckst homology domain, C1 domain, guanine-nucleotide
           releasing FA metal-binding; 2.73A {Homo sapiens} PDB:
           2d86_A
          Length = 587

 Score = 24.6 bits (53), Expect = 4.8
 Identities = 8/25 (32%), Positives = 15/25 (60%), Gaps = 2/25 (8%)

Query: 60  HRTYSCVHCRAHLASHDELISKIPR 84
           ++ Y C  CRA  ++H E + ++P 
Sbjct: 544 YQGYRCHRCRA--SAHKECLGRVPP 566


>3ivr_A Putative long-chain-fatty-acid COA ligase; structural genomics,
           PSI-2, protein S initiative, fatty acid synthesis; HET:
           GOL; 2.00A {Rhodopseudomonas palustris}
          Length = 509

 Score = 24.4 bits (54), Expect = 4.9
 Identities = 3/18 (16%), Positives = 7/18 (38%), Gaps = 5/18 (27%)

Query: 67  HCRAHLASHDELISKIPR 84
              + +A +     K P+
Sbjct: 462 FVASLIARY-----KKPK 474


>4fuq_A Malonyl COA synthetase; ANL superfamily, methylma malonate, ligase;
           HET: MSE; 1.70A {Rhodopseudomonas palustris} PDB:
           4fut_A*
          Length = 503

 Score = 24.5 bits (54), Expect = 4.9
 Identities = 4/18 (22%), Positives = 6/18 (33%), Gaps = 5/18 (27%)

Query: 67  HCRAHLASHDELISKIPR 84
                LA       K+P+
Sbjct: 461 GLDGQLAKF-----KMPK 473


>3tig_A TTL protein; ATP-grAsp, ligase, tubulin; 2.50A {Silurana} PDB:
           3tii_A* 3tin_A*
          Length = 380

 Score = 24.2 bits (52), Expect = 7.2
 Identities = 3/30 (10%), Positives = 7/30 (23%), Gaps = 3/30 (10%)

Query: 42  QQLSNIMVKTFQA---YLPNCHRTYSCVHC 68
            Q+  I+          +   +  Y     
Sbjct: 288 CQIKEIIRVCLSCLEPAISTKYLPYHSFQL 317


>2v7b_A Benzoate-coenzyme A ligase; benzoate oxidation, benzoate COA
           ligase; 1.84A {Burkholderia xenovorans}
          Length = 529

 Score = 24.1 bits (53), Expect = 8.4
 Identities = 6/18 (33%), Positives = 7/18 (38%), Gaps = 5/18 (27%)

Query: 67  HCRAHLASHDELISKIPR 84
             +  LA H     K PR
Sbjct: 493 FVKDRLAPH-----KYPR 505


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.321    0.131    0.431 

Gapped
Lambda     K      H
   0.267   0.0789    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,240,207
Number of extensions: 54145
Number of successful extensions: 146
Number of sequences better than 10.0: 1
Number of HSP's gapped: 146
Number of HSP's successfully gapped: 12
Length of query: 84
Length of database: 6,701,793
Length adjustment: 52
Effective length of query: 32
Effective length of database: 5,249,901
Effective search space: 167996832
Effective search space used: 167996832
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 (21.9 bits)
S2: 51 (23.3 bits)