RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12163
         (88 letters)



>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 = 39.6 bits (92), Expect = 3e-05
 Identities = 20/93 (21%), Positives = 35/93 (37%), Gaps = 23/93 (24%)

Query: 10  LAASVI--SSIYSYIWDIKMDWGLFDKNAPPDNPFLREETVYSSTTS-TLIG------YV 60
           L  + +    +++   +I ++W L + +  PD  +L      S   S  LIG      YV
Sbjct: 198 LIRTTLDAEKVFTQGLNI-LEW-LENPSNTPDKDYLL-----SIPISCPLIGVIQLAHYV 250

Query: 61  LF------NPTGILMIQFLQSITCLGGVVKTLA 87
           +        P G L      +     G+V  +A
Sbjct: 251 VTAKLLGFTP-GELRSYLKGATGHSQGLVTAVA 282


>3dkb_A Tumor necrosis factor, alpha-induced protein 3; OTU domain, DUB
           domain, apoptosis, cytoplasm, DNA-binding, hydrolase,
           metal-binding, nucleus; 2.50A {Homo sapiens} PDB: 2vfj_A
          Length = 390

 Score = 24.4 bits (52), Expect = 6.4
 Identities = 9/47 (19%), Positives = 15/47 (31%), Gaps = 1/47 (2%)

Query: 6   FYPWLAASVISSIYSY-IWDIKMDWGLFDKNAPPDNPFLREETVYSS 51
                +   + +   Y   +   +W    K A  D P  R    Y+S
Sbjct: 164 LESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTPMARSGLQYNS 210


>2ipq_X Hypothetical protein STY4665; structural genomics, unknown
           function, PSI, protein structur initiative; 2.20A
           {Salmonella typhi} SCOP: a.4.5.74
          Length = 135

 Score = 23.9 bits (51), Expect = 7.4
 Identities = 8/20 (40%), Positives = 11/20 (55%)

Query: 25  IKMDWGLFDKNAPPDNPFLR 44
           IKM     + N P D+ FL+
Sbjct: 113 IKMSEIYANGNFPDDSLFLK 132


>3das_A Putative oxidoreductase; aldose sugar dehydrogenase, beta
           propellor, PQQ, SGDH; HET: MSE ARA PQQ; 1.60A
           {Streptomyces coelicolor}
          Length = 347

 Score = 23.8 bits (52), Expect = 9.5
 Identities = 8/18 (44%), Positives = 8/18 (44%), Gaps = 1/18 (5%)

Query: 33  DKNAPPDNPFLREETVYS 50
           D    P NPF     VYS
Sbjct: 182 DGEPAPGNPFPGSP-VYS 198


>3fqm_A NS5A, non-structural protein 5A; HCV, domain I, phosphoprotein,
           RNA-binding, metal BIND protein; 1.90A {Hepatitis c
           virus} PDB: 3fqq_A* 1zh1_A
          Length = 177

 Score = 23.8 bits (51), Expect = 9.6
 Identities = 7/15 (46%), Positives = 8/15 (53%)

Query: 36  APPDNPFLREETVYS 50
           AP   P LREE  + 
Sbjct: 132 APACKPLLREEVTFL 146


>3a9g_A Putative uncharacterized protein; PQQ dependent dehydrogenase,
           aldose sugar dehydrogenase, BET propeller fold,
           oxidoreductase; HET: TRE; 2.39A {Pyrobaculum aerophilum}
           PDB: 3a9h_A*
          Length = 354

 Score = 23.8 bits (52), Expect = 9.6
 Identities = 6/18 (33%), Positives = 9/18 (50%), Gaps = 1/18 (5%)

Query: 33  DKNAPPDNPFLREETVYS 50
           +   P DNPF     ++S
Sbjct: 177 EGRPPADNPFPNSP-IWS 193


  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
   0.324    0.140    0.462 

Gapped
Lambda     K      H
   0.267   0.0725    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,361,141
Number of extensions: 63945
Number of successful extensions: 135
Number of sequences better than 10.0: 1
Number of HSP's gapped: 135
Number of HSP's successfully gapped: 9
Length of query: 88
Length of database: 6,701,793
Length adjustment: 56
Effective length of query: 32
Effective length of database: 5,138,217
Effective search space: 164422944
Effective search space used: 164422944
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: 51 (23.4 bits)