RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy53
         (78 letters)



>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 30.2 bits (67), Expect = 0.051
 Identities = 16/77 (20%), Positives = 24/77 (31%), Gaps = 19/77 (24%)

Query: 1   MDIYFNQLRENIVRGQP----------PDKQASMVQW----FENLMNSIER--NLLTKN- 43
           +D     L   ++   P           D  A+   W     + L   IE   N+L    
Sbjct: 311 LDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAE 370

Query: 44  -RDRFTQNLSMFRRDIN 59
            R  F   LS+F    +
Sbjct: 371 YRKMF-DRLSVFPPSAH 386


>1d8w_A L-rhamnose isomerase; beta-alpha-8-barrels, aldose-ketose
           isomerization, hydride shift; 1.60A {Escherichia coli}
           SCOP: c.1.15.2 PDB: 1de5_A* 1de6_A*
          Length = 426

 Score = 25.7 bits (56), Expect = 1.5
 Identities = 7/25 (28%), Positives = 12/25 (48%)

Query: 12  IVRGQPPDKQASMVQWFENLMNSIE 36
           IVR    D+    + +F+  +N I 
Sbjct: 319 IVRHDLFDRVHIGLDFFDASINRIA 343


>3rau_A Tyrosine-protein phosphatase non-receptor type 23; BRO1 domain,
           hydrolase; 1.95A {Homo sapiens}
          Length = 363

 Score = 25.2 bits (54), Expect = 2.4
 Identities = 8/29 (27%), Positives = 12/29 (41%)

Query: 4   YFNQLRENIVRGQPPDKQASMVQWFENLM 32
            F  LRE+  +    D    ++    NLM
Sbjct: 155 AFAYLREHFPQAYSVDMSRQILTLNVNLM 183


>1zb1_A BRO1 protein; AIP1, BRO1 domain, SNF7, trafficking, protein
           transport; 1.95A {Saccharomyces cerevisiae}
          Length = 392

 Score = 24.8 bits (53), Expect = 3.2
 Identities = 7/29 (24%), Positives = 12/29 (41%)

Query: 4   YFNQLRENIVRGQPPDKQASMVQWFENLM 32
            F  L EN +     D Q+   ++  N+ 
Sbjct: 158 CFEYLSENFLNSPSVDLQSENTRFLANIC 186


>3fmt_A Protein SEQA; protein-DNA complex, hemimethylated GATC, DNA
          replication; HET: 6MA; 2.98A {Escherichia coli}
          Length = 162

 Score = 24.5 bits (53), Expect = 3.4
 Identities = 12/55 (21%), Positives = 19/55 (34%)

Query: 2  DIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRR 56
          DI    L+ +    +P       V+    L+ S E     +  +RF   LS    
Sbjct: 27 DILRRMLKFSAASQKPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYS 81


>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 = 3.9
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 14/68 (20%)

Query: 2   DIYFNQLRENIVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDR---FTQNLSMFRRDI 58
           D YF +LR+ + +         +V             L+    D    FTQ L     +I
Sbjct: 167 DDYFEELRD-LYQTYHV-----LVGDLIKFSAETLSELIRTTLDAEKVFTQGL-----NI 215

Query: 59  NDSLKGPN 66
            + L+ P+
Sbjct: 216 LEWLENPS 223


>1rw3_A POL polyprotein; RNA and DNA dependent DNA polymerase, reverse
           transcriptase, transferase, replication; 3.00A {Moloney
           murine leukemia virus} SCOP: e.8.1.2
          Length = 455

 Score = 24.6 bits (54), Expect = 4.2
 Identities = 2/20 (10%), Positives = 8/20 (40%)

Query: 28  FENLMNSIERNLLTKNRDRF 47
           F+  ++    +   ++ D  
Sbjct: 180 FDEALHRDLADFRIQHPDLI 199


>1lrr_A SEQA protein; protein-DNA complex, replication, methylated GATC,
          replication inhibitor/DNA complex; HET: 6MA; 2.65A
          {Escherichia coli} SCOP: d.228.1.1
          Length = 131

 Score = 24.1 bits (52), Expect = 5.7
 Identities = 11/45 (24%), Positives = 16/45 (35%)

Query: 12 IVRGQPPDKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRR 56
          IV  +P       V+    L+ S E     +  +RF   LS    
Sbjct: 6  IVEAKPVKTIKDKVRAMRELLLSDEYAEQKRAVNRFMLLLSTLYS 50


>2bbh_A Divalent cation transport-related protein; transporter, Mg,
           membrane, structural genomics, structural G consortium,
           SGC; HET: DMU; 1.85A {Thermotoga maritima} SCOP:
           d.328.1.1
          Length = 269

 Score = 23.8 bits (52), Expect = 6.4
 Identities = 5/41 (12%), Positives = 18/41 (43%)

Query: 19  DKQASMVQWFENLMNSIERNLLTKNRDRFTQNLSMFRRDIN 59
           D    +++  ++ ++ +E  +L +      Q     +R++ 
Sbjct: 182 DDYFVLLEKIDDEIDVLEEEVLERPEKETVQRTHQLKRNLV 222


>2p1h_A APAF-1, apoptotic protease-activating factor 1; folding,
          unfolding, apoptosis; 1.59A {Homo sapiens} SCOP:
          a.77.1.3 PDB: 1cww_A 1c15_A 1cy5_A 3ygs_C 2ygs_A
          Length = 94

 Score = 23.5 bits (51), Expect = 6.8
 Identities = 5/20 (25%), Positives = 13/20 (65%)

Query: 32 MNSIERNLLTKNRDRFTQNL 51
          M++  RN L ++R+   +++
Sbjct: 3  MDAKARNCLLQHREALEKDI 22


  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    0.131    0.382 

Gapped
Lambda     K      H
   0.267   0.0639    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,090,696
Number of extensions: 45229
Number of successful extensions: 131
Number of sequences better than 10.0: 1
Number of HSP's gapped: 131
Number of HSP's successfully gapped: 12
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 (23.6 bits)