RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13888
         (70 letters)



>3dw8_B Serine/threonine-protein phosphatase 2A 55 kDa RE subunit B alpha
           isoform; holoenzyme, PR55, WD repeat, hydrolase, iron,
           manganese binding, methylation, phosphoprotein, protein
           phosphatase; HET: 1ZN; 2.85A {Homo sapiens}
          Length = 447

 Score = 66.7 bits (162), Expect = 4e-15
 Identities = 46/56 (82%), Positives = 48/56 (85%)

Query: 1   SKTSIPKRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLRRKNQAHFLLSTND 56
           +K     RGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWL +KN A FLLSTND
Sbjct: 61  NKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTND 116


>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 = 29.4 bits (65), Expect = 0.068
 Identities = 18/85 (21%), Positives = 31/85 (36%), Gaps = 32/85 (37%)

Query: 11  YNVYSTFQSHE----PEFDY--------LKSLEIEEKINK-------IRWLRRK------ 45
           YN+  TF S +        Y        LK++E  E++          R+L +K      
Sbjct: 453 YNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPERMTLFRMVFLDFRFLEQKIRHDST 512

Query: 46  --NQAHFLLST-NDFEFLIFIYSRF 67
             N +  +L+T    +F    Y  +
Sbjct: 513 AWNASGSILNTLQQLKF----YKPY 533


>1jb0_D Photosystem 1 reaction centre subunit II; membrane protein,
           multiprotein-pigment complex, photosynthes; HET: CL1 PQN
           BCR LHG LMG; 2.50A {Synechococcus elongatus} SCOP:
           d.187.1.1 PDB: 3pcq_D*
          Length = 138

 Score = 26.1 bits (57), Expect = 0.75
 Identities = 11/41 (26%), Positives = 15/41 (36%)

Query: 6   PKRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLRRKN 46
            K  +Y +Y  F   E    + K     EK+NK R      
Sbjct: 75  RKINDYKIYRIFPDGETVLIHPKDGVFPEKVNKGREAVNSV 115


>3do6_A Formate--tetrahydrofolate ligase; TM1766, putative
           formyltetrahydrofolate synthetase, structural genomics;
           HET: MSE; 1.85A {Thermotoga maritima}
          Length = 543

 Score = 25.2 bits (56), Expect = 1.6
 Identities = 7/27 (25%), Positives = 13/27 (48%)

Query: 13  VYSTFQSHEPEFDYLKSLEIEEKINKI 39
           V    +  EP + Y  +  +E+KI  +
Sbjct: 412 VAEAAKDVEPAYLYEMNDPVEKKIEIL 438


>3pzx_A Formate--tetrahydrofolate ligase; HET: TOE; 2.20A {Moorella
           thermoacetica} PDB: 1fp7_A 1fpm_A* 3qb6_A* 3qus_A*
           3rbo_A* 3sin_A* 1eg7_A
          Length = 557

 Score = 24.8 bits (55), Expect = 2.4
 Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)

Query: 13  VYSTFQSHEPEFDYLKSLE--IEEKINKI 39
           V  T +S    F  L +L+  I++KI KI
Sbjct: 424 VLQTLESRPSNFHVLYNLDLSIKDKIAKI 452


>2wsc_D Photosystem I reaction center subunit II, chloroplastic;
           photosynthesis, electron transfer, membrane proteins,
           large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A
           {Spinacia oleracea} PDB: 2wse_D* 2wsf_D* 2o01_D* 3lw5_D*
          Length = 212

 Score = 24.8 bits (53), Expect = 2.5
 Identities = 10/31 (32%), Positives = 15/31 (48%)

Query: 10  EYNVYSTFQSHEPEFDYLKSLEIEEKINKIR 40
           +Y  Y  F S E ++ + K     EK+N  R
Sbjct: 153 KYQFYRVFPSGEVQYLHPKDGVYPEKVNPGR 183


>3bbn_M Ribosomal protein S13; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 145

 Score = 23.8 bits (52), Expect = 4.8
 Identities = 5/16 (31%), Positives = 10/16 (62%)

Query: 33  EEKINKIRWLRRKNQA 48
           EE++  +R  +R N+ 
Sbjct: 94  EEEVIILRKEKRFNRV 109


>1r5l_A Alpha-TTP, protein (alpha-tocopherol transfer protein); ataxia
          with vitamin E deficiency, transport protein; HET: MSE
          VIV; 1.50A {Homo sapiens} SCOP: a.5.3.1 c.13.1.1 PDB:
          1oiz_A* 1oip_A*
          Length = 262

 Score = 23.8 bits (52), Expect = 5.9
 Identities = 7/37 (18%), Positives = 13/37 (35%), Gaps = 1/37 (2%)

Query: 31 EIEEKINKIR-WLRRKNQAHFLLSTNDFEFLIFIYSR 66
           ++  +  +R   R        L   D   L F+ +R
Sbjct: 7  LLQPGLAALRRRAREAGVPLAPLPLTDSFLLRFLRAR 43


>3ces_A MNMG, tRNA uridine 5-carboxymethylaminomethyl modificat GIDA, GIDA;
           tRNA modification, FAD binding domain, structural
           genomics; 2.41A {Escherichia coli} PDB: 3cp2_A 3g05_A
          Length = 651

 Score = 23.6 bits (52), Expect = 6.2
 Identities = 6/23 (26%), Positives = 10/23 (43%), Gaps = 4/23 (17%)

Query: 22  PEFDYLK----SLEIEEKINKIR 40
              DY +    S E+  K+N  +
Sbjct: 594 ATLDYRQVSGLSNEVIAKLNDHK 616


>2hhc_A NODZ, nodulation fucosyltransferase NODZ; glycosyltransferase;
           1.54A {Bradyrhizobium SP} PDB: 2hlh_A 2ocx_A* 3siw_A*
           3six_A*
          Length = 330

 Score = 23.6 bits (50), Expect = 6.5
 Identities = 9/62 (14%), Positives = 19/62 (30%), Gaps = 1/62 (1%)

Query: 7   KRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLRRKNQAHFLLSTNDFEFLIFIYSR 66
           + G          +  + +     ++   I K + L         L T+  + L  +   
Sbjct: 177 RHGNGEDIMEHAPYWADSELALH-QVCMAIRKAKALSYPKPVKVFLCTDSAQVLDQVSGL 235

Query: 67  FP 68
           FP
Sbjct: 236 FP 237


>3cp8_A TRNA uridine 5-carboxymethylaminomethyl modification enzyme GIDA;
           rossmann fold, FAD-binding domain, dinucleotide-binding
           motif; HET: FAD; 3.20A {Chlorobium tepidum}
          Length = 641

 Score = 23.6 bits (52), Expect = 6.9
 Identities = 8/23 (34%), Positives = 10/23 (43%), Gaps = 4/23 (17%)

Query: 22  PEFDYLK----SLEIEEKINKIR 40
             F+Y      S E  EK+ K R
Sbjct: 592 DNFNYDSLNSLSSEGREKLLKHR 614


>2zxi_A TRNA uridine 5-carboxymethylaminomethyl modificat MNMG;
           modification, 5-carboxymethylaminomethyl uridine, WOBB
           uridine, FAD; HET: FAD; 2.30A {Aquifex aeolicus} PDB:
           2zxh_A* 2e57_A*
          Length = 637

 Score = 23.6 bits (52), Expect = 8.0
 Identities = 8/23 (34%), Positives = 12/23 (52%), Gaps = 4/23 (17%)

Query: 22  PEFDYLK----SLEIEEKINKIR 40
           P+ DY K    + E  EK+ K +
Sbjct: 586 PDIDYDKIPGLTKEAREKLKKFK 608


>4ecm_A Glucose-1-phosphate thymidylyltransferase; HET: DAU; 2.30A
           {Bacillus anthracis} PDB: 3hl3_A*
          Length = 269

 Score = 23.3 bits (51), Expect = 8.5
 Identities = 6/13 (46%), Positives = 7/13 (53%)

Query: 23  EFDYLKSLEIEEK 35
                K +EIEEK
Sbjct: 170 NIQNRKIIEIEEK 182


  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
   0.323    0.138    0.414 

Gapped
Lambda     K      H
   0.267   0.0812    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,049,965
Number of extensions: 46319
Number of successful extensions: 140
Number of sequences better than 10.0: 1
Number of HSP's gapped: 140
Number of HSP's successfully gapped: 16
Length of query: 70
Length of database: 6,701,793
Length adjustment: 40
Effective length of query: 30
Effective length of database: 5,584,953
Effective search space: 167548590
Effective search space used: 167548590
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)