RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11838
         (78 letters)



>2xex_A Elongation factor G; GTPase, translation, biosynthetic protein;
           1.90A {Staphylococcus aureus}
          Length = 693

 Score = 63.3 bits (155), Expect = 7e-14
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 5   MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHK 49
           MGELHL+I+ DR+  E+ +E ++G   ++Y+ET  S A    +  
Sbjct: 453 MGELHLDILVDRMKKEFNVECNVGAPMVSYRETFKSSAQVQGKFS 497


>1dar_A EF-G, elongation factor G; ribosomal translocase, translational
           GTPase; HET: GDP; 2.40A {Thermus thermophilus} SCOP:
           b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 PDB: 1elo_A 1ktv_A
           2om7_L* 2wri_Y* 2wrk_Y* 2xsy_Y* 2xuy_Y* 2j7k_A* 2efg_A*
           1jqm_B 1efg_A* 1fnm_A* 1pn6_A 2bm1_A* 2bm0_A* 2bv3_A*
           3izp_E 1zn0_B 1jqs_C 2bcw_C ...
          Length = 691

 Score = 62.9 bits (154), Expect = 1e-13
 Identities = 21/45 (46%), Positives = 31/45 (68%)

Query: 5   MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHK 49
           MGELHLEII DR+  E+K++A++G  Q+AY+ET+  P     +  
Sbjct: 454 MGELHLEIIVDRLKREFKVDANVGKPQVAYRETITKPVDVEGKFI 498


>2rdo_7 EF-G, elongation factor G; elongation factor G, EF-G, RRF, GDPNP,
           50S subunit, cryo-EM, REAL-space refinement,
           ribonucleoprotein; 9.10A {Escherichia coli} PDB: 3j0e_H
          Length = 704

 Score = 60.6 bits (148), Expect = 7e-13
 Identities = 21/47 (44%), Positives = 30/47 (63%), Gaps = 1/47 (2%)

Query: 5   MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHKIK 51
           MGELHL+II DR+  E+ +EA++G  Q+AY+ET+        E K  
Sbjct: 461 MGELHLDIIVDRMKREFNVEANVGKPQVAYRETIRQKV-TDVEGKHA 506


>2dy1_A Elongation factor G; translocation, GTP complex, structural
           genomics, NPPSFA; HET: GTP; 1.60A {Thermus thermophilus}
           SCOP: b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1
           PDB: 1wdt_A*
          Length = 665

 Score = 59.8 bits (146), Expect = 1e-12
 Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 1/45 (2%)

Query: 5   MGELHLEIIRDRILTEYKIEADLGPLQIAYKETVLSPAMASHEHK 49
            GELHL   ++R L +Y +E +    ++ Y+ET+   A    ++K
Sbjct: 428 HGELHLATAKER-LQDYGVEVEFSVPKVPYRETIKKVAEGQGKYK 471


>1n0u_A EF-2, elongation factor 2; G-protein, CIS-proline, translation;
           HET: SO1; 2.12A {Saccharomyces cerevisiae} SCOP:
           b.43.3.1 c.37.1.8 d.14.1.1 d.58.11.1 d.58.11.1 PDB:
           1n0v_C 1s1h_T 2e1r_A* 2npf_A* 2p8w_T* 3dny_T 3b82_A*
           1zm2_A* 1zm3_A* 1zm4_A* 1zm9_A* 2p8x_T* 2p8y_T* 2p8z_T*
           2zit_A* 1u2r_A* 3b78_A* 3b8h_A*
          Length = 842

 Score = 36.2 bits (83), Expect = 4e-04
 Identities = 15/46 (32%), Positives = 24/46 (52%), Gaps = 1/46 (2%)

Query: 5   MGELHLEIIRDRILTEY-KIEADLGPLQIAYKETVLSPAMASHEHK 49
            GELHLEI    +  ++  +   + P  +AY+ETV S +  +   K
Sbjct: 533 TGELHLEICLQDLEHDHAGVPLKISPPVVAYRETVESESSQTALSK 578


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
          photosynthetic reaction center, peripheral antenna;
          HET: CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 29.1 bits (64), Expect = 0.092
 Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 3/24 (12%)

Query: 51 KIGKSFRLRFRDDKT--LAVKTSV 72
          K+  S +L + DD    LA+K ++
Sbjct: 24 KLQASLKL-YADDSAPALAIKATM 46



 Score = 26.8 bits (58), Expect = 0.54
 Identities = 7/24 (29%), Positives = 13/24 (54%), Gaps = 7/24 (29%)

Query: 22 KIEADLGPLQIAYK-ETVLSPAMA 44
          K++A L      Y  ++  +PA+A
Sbjct: 24 KLQASLKL----YADDS--APALA 41


>2ywe_A GTP-binding protein LEPA; G domain, beta-barrel, ferredoxin-like
           domain, structural GE NPPSFA; 2.05A {Aquifex aeolicus}
           PDB: 2ywf_A* 2ywg_A* 2ywh_A*
          Length = 600

 Score = 27.8 bits (63), Expect = 0.30
 Identities = 8/19 (42%), Positives = 15/19 (78%)

Query: 6   GELHLEIIRDRILTEYKIE 24
           G LH+EI+++R+  EY ++
Sbjct: 346 GLLHMEIVQERLEREYGVK 364


>3cb4_D GTP-binding protein LEPA; GTPase, OB-fold, membrane,
           nucleotide-binding, translation; 2.80A {Escherichia
           coli} PDB: 3deg_C*
          Length = 599

 Score = 27.4 bits (62), Expect = 0.35
 Identities = 9/19 (47%), Positives = 15/19 (78%)

Query: 6   GELHLEIIRDRILTEYKIE 24
           G LH+EII++R+  EY ++
Sbjct: 344 GLLHMEIIQERLEREYDLD 362


>2h5e_A Peptide chain release factor RF-3; beta barrel, translation; HET:
           GDP; 2.80A {Escherichia coli} PDB: 2o0f_A 3sfs_W*
           3zvo_Y* 3uoq_W*
          Length = 529

 Score = 27.4 bits (61), Expect = 0.43
 Identities = 8/28 (28%), Positives = 16/28 (57%)

Query: 6   GELHLEIIRDRILTEYKIEADLGPLQIA 33
           G L  +++  R+ +EY +EA    + +A
Sbjct: 442 GVLQFDVVVARLKSEYNVEAVYESVNVA 469


>3tr5_A RF-3, peptide chain release factor 3; protein synthesis,
           translation; HET: GDP; 2.11A {Coxiella burnetii}
          Length = 528

 Score = 27.4 bits (61), Expect = 0.45
 Identities = 5/28 (17%), Positives = 13/28 (46%)

Query: 6   GELHLEIIRDRILTEYKIEADLGPLQIA 33
           G L  +++  R+  EY ++     + + 
Sbjct: 441 GLLQFDVVAYRLENEYNVKCVYESVNVV 468


>2vqe_M 30S ribosomal protein S13, 30S ribosomal protein S6;
          tRNA-binding, rRNA-binding, metal-binding, zinc-finger,
          translation; HET: TM2 PAR; 2.5A {Thermus thermophilus}
          SCOP: a.156.1.1 PDB: 1gix_P* 1hnw_M* 1hnx_M* 1hnz_M*
          1hr0_M 1ibk_M* 1ibl_M* 1ibm_M 1j5e_M 1jgo_P* 1jgp_P*
          1jgq_P* 1mj1_P* 1ml5_P* 1n32_M* 1n33_M* 1n34_M 1n36_M
          1xmo_M* 1xmq_M* ...
          Length = 126

 Score = 24.4 bits (54), Expect = 3.1
 Identities = 6/28 (21%), Positives = 15/28 (53%), Gaps = 3/28 (10%)

Query: 3  KRMGEL---HLEIIRDRILTEYKIEADL 27
           R+ +L    +  +R+ +   +K+E +L
Sbjct: 43 TRVKDLTEAEVVRLREYVENTWKLEGEL 70


>1x9n_A DNA ligase I; 5'-adenylated nicked DNA, protein-DNA complex, L
           complex; HET: DNA DOC AMP; 3.00A {Homo sapiens} SCOP:
           a.235.1.1 b.40.4.6 d.142.2.1
          Length = 688

 Score = 24.5 bits (53), Expect = 4.5
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 6/54 (11%)

Query: 30  LQIAYKETVLSPAMASHEHKIKIGKSFRLRF------RDDKTLAVKTSVAECED 77
            ++   +  LSP   +    +   K   LRF      R+DK     T+ A+   
Sbjct: 611 WEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPEQATTSAQVAC 664


>2hiv_A Thermostable DNA ligase; ATP-dependent, open conformation; 2.05A
           {Sulfolobus solfataricus} PDB: 2hix_A*
          Length = 621

 Score = 24.0 bits (52), Expect = 6.7
 Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 6/54 (11%)

Query: 30  LQIAYKETVLSPAMASHEHKIKIGKSFRLRF------RDDKTLAVKTSVAECED 77
            +I   E  +SP     +  ++      +RF      RDDK+    T+  E  +
Sbjct: 549 AEIIGSEITISPLHTCCQDVVEKDAGLSIRFPRFIRWRDDKSPEDATTTDEILE 602


  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
   0.319    0.135    0.372 

Gapped
Lambda     K      H
   0.267   0.0688    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,148,303
Number of extensions: 55085
Number of successful extensions: 91
Number of sequences better than 10.0: 1
Number of HSP's gapped: 87
Number of HSP's successfully gapped: 18
Length of query: 78
Length of database: 6,701,793
Length adjustment: 47
Effective length of query: 31
Effective length of database: 5,389,506
Effective search space: 167074686
Effective search space used: 167074686
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: 51 (23.5 bits)