RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy930
         (89 letters)



>3l1l_A Arginine/agmatine antiporter; TCDB 2.A.3.2.5, ADIC, Arg-bound,
           amino-acid transport, cell inner membrane, cell
           membrane, membrane; HET: ARG BNG; 3.00A {Escherichia
           coli} PDB: 3h5m_A* 3h6b_A 3lrb_A 3lrc_A 3ob6_A* 3hqk_A
           3ncy_A
          Length = 445

 Score = 47.7 bits (114), Expect = 4e-08
 Identities = 17/79 (21%), Positives = 28/79 (35%), Gaps = 3/79 (3%)

Query: 1   MIPKSGGDYAYINEAFGPLPAFLYMWVALFVIMPTGNAVTALTFAQYILQPIWPHCDPPY 60
           + P  GG YAY    FGP   +       ++    GN    +    Y L   +P    P+
Sbjct: 66  LDPSPGGSYAYARRCFGPFLGYQTNV-LYWLACWIGNIAMVVIGVGY-LSYFFPILKDPW 123

Query: 61  SAVRLLAAVITCLLTAINC 79
               +   V+  +   +N 
Sbjct: 124 VLT-ITCVVVLWIFVLLNI 141


>3gia_A Uncharacterized protein MJ0609; membrane protein, transporter, cell
           membrane, membrane, transmembrane, transport protein;
           HET: D10 BCN; 2.32A {Methanocaldococcus jannaschii} PDB:
           3gi9_C* 3gi8_C
          Length = 444

 Score = 43.5 bits (103), Expect = 1e-06
 Identities = 18/81 (22%), Positives = 31/81 (38%), Gaps = 4/81 (4%)

Query: 1   MIPKSGGDYAYINEAFGP-LPAFLYMWVALFVIMPTGNAVTALTFAQYILQPIWPHCDPP 59
            I  + G  A+I++A G  +         L++      A+ A  FA Y L  I  +    
Sbjct: 65  KIVSNAGPIAFIHKAIGDNIITGALSI-LLWMSYVISIALFAKGFAGYFLPLI--NAPIN 121

Query: 60  YSAVRLLAAVITCLLTAINCY 80
              + +    I    TA+N +
Sbjct: 122 TFNIAITEIGIVAFFTALNFF 142


>4djk_A Probable glutamate/gamma-aminobutyrate antiporter; LEUT,
           glutamate-GABA antiporter, transport protein; 3.10A
           {Escherichia coli} PDB: 4dji_A
          Length = 511

 Score = 36.0 bits (83), Expect = 6e-04
 Identities = 12/78 (15%), Positives = 26/78 (33%), Gaps = 2/78 (2%)

Query: 3   PKSGGDYAYINEAFGPLPAFLYMWVALFVIMPTGNAVTALTFAQYILQPI-WPHCDPPYS 61
            + GG +A+++   GP   F  +    ++ +  G           +   + WP  +    
Sbjct: 70  WEEGGVFAWVSNTLGPRWGFAAISF-GYLQIAIGFIPMLYFVLGALSYILKWPALNEDPI 128

Query: 62  AVRLLAAVITCLLTAINC 79
              + A +I   L     
Sbjct: 129 TKTIAALIILWALALTQF 146


>2v1x_A ATP-dependent DNA helicase Q1; DNA strand annealing, mismatch
          repair, nucleotide-binding, DNA-binding, polymorphism,
          nuclear protein, ATPase; HET: ADP; 2.00A {Homo sapiens}
          PDB: 2wwy_A*
          Length = 591

 Score = 24.9 bits (55), Expect = 4.6
 Identities = 5/7 (71%), Positives = 7/7 (100%)

Query: 30 FVIMPTG 36
          F++MPTG
Sbjct: 63 FLVMPTG 69


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
          acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
          synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
          Length = 2006

 Score = 24.6 bits (53), Expect = 5.5
 Identities = 8/41 (19%), Positives = 14/41 (34%), Gaps = 8/41 (19%)

Query: 34 PTGNAVTAL----TFAQYILQP---IWPHCDPPYSAVRLLA 67
          PT +   A      F + + +P        D P +   L+ 
Sbjct: 23 PTASFFIASQLQEQFNKILPEPTEGFAAD-DEPTTPAELVG 62



 Score = 24.2 bits (52), Expect = 8.3
 Identities = 11/64 (17%), Positives = 15/64 (23%), Gaps = 24/64 (37%)

Query: 20   PAFLYMWVALFVIM------PTGNAV--------TALT-FAQYILQPIWPHCDPPYSAVR 64
            PA   M  A F  +      P              AL   A  +            S V 
Sbjct: 1734 PALTLMEKAAFEDLKSKGLIPADATFAGHSLGEYAALASLADVM---------SIESLVE 1784

Query: 65   LLAA 68
            ++  
Sbjct: 1785 VVFY 1788


>3flo_B DNA polymerase alpha catalytic subunit A; protein-protein
          complex, phosphoesterase fold, OB fold, zinc-binding
          motif, DNA replication; HET: DNA; 2.50A {Saccharomyces
          cerevisiae}
          Length = 206

 Score = 23.9 bits (51), Expect = 9.6
 Identities = 7/35 (20%), Positives = 16/35 (45%)

Query: 54 PHCDPPYSAVRLLAAVITCLLTAINCYNKYHLTCS 88
           HC+  ++ ++L + +   +   I+ Y    L C 
Sbjct: 53 KHCEQLFTPLQLTSQIEHSIRAHISLYYAGWLQCD 87


  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
   0.329    0.141    0.479 

Gapped
Lambda     K      H
   0.267   0.0616    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,402,865
Number of extensions: 68401
Number of successful extensions: 175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 174
Number of HSP's successfully gapped: 12
Length of query: 89
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 32
Effective length of database: 5,110,296
Effective search space: 163529472
Effective search space used: 163529472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (23.7 bits)