RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13383
         (105 letters)



>2gd5_A Charged multivesicular BODY protein 3; CHMP3, ESCRT-III, protein
          transport; 2.80A {Homo sapiens} PDB: 3frv_A
          Length = 179

 Score = 52.4 bits (125), Expect = 5e-10
 Identities = 14/49 (28%), Positives = 31/49 (63%)

Query: 8  KITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQM 56
          +  P+E++ +    + K MR +DR+ + ++++E+K+   +K  AK+GQ 
Sbjct: 5  EKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQK 53


>3frt_A Charged multivesicular BODY protein 3; ESCRT, ESCRT-111, CHMP,
          IST1, coiled coil, cytoplasm, lipoprotein, membrane,
          myristate, phosphoprotein; 4.00A {Homo sapiens}
          Length = 218

 Score = 52.1 bits (124), Expect = 1e-09
 Identities = 14/51 (27%), Positives = 32/51 (62%)

Query: 6  GRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQM 56
           ++  P+E++ +    + K MR +DR+ + ++++E+K+   +K  AK+GQ 
Sbjct: 3  MQEKPPKELVNEWSLKIRKEMRVVDRQIRDIQREEEKVKRSVKDAAKKGQK 53


>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 = 32.6 bits (73), Expect = 0.011
 Identities = 10/28 (35%), Positives = 14/28 (50%), Gaps = 4/28 (14%)

Query: 32 EKQHMEQQEKKLIADIKKMAKEGQMTLS 59
          EKQ +    KKL A +K  A +    L+
Sbjct: 18 EKQAL----KKLQASLKLYADDSAPALA 41


>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 = 32.5 bits (73), Expect = 0.016
 Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 5/67 (7%)

Query: 3   WL-FGRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMTLSTE 61
           WL      +PE +L   Q+ L +   +      H     K  I  I+    E +  L ++
Sbjct: 186 WLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHS-SNIKLRIHSIQ---AELRRLLKSK 241

Query: 62  RHVALLL 68
            +   LL
Sbjct: 242 PYENCLL 248



 Score = 30.6 bits (68), Expect = 0.068
 Identities = 18/93 (19%), Positives = 38/93 (40%), Gaps = 15/93 (16%)

Query: 10  TPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADIKKMAKEGQMTLSTERHVAL--- 66
           TP+E+     + L+   +DL RE   +     + ++ I +  ++G  T    +HV     
Sbjct: 299 TPDEVKSLLLKYLDCRPQDLPRE---VLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKL 355

Query: 67  --LLEFVIIVGPENRENFENSDLRPQSNFFAVF 97
             ++E  +          E ++ R   +  +VF
Sbjct: 356 TTIIESSL-------NVLEPAEYRKMFDRLSVF 381



 Score = 25.6 bits (55), Expect = 4.3
 Identities = 10/88 (11%), Positives = 27/88 (30%), Gaps = 26/88 (29%)

Query: 3   WLFGRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQE---KKLIADIKK---------- 49
           +L  +KI  +        ++   ++ L   K ++   +   ++L+  I            
Sbjct: 502 FL-EQKIRHDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEENLI 560

Query: 50  ------------MAKEGQMTLSTERHVA 65
                       MA++  +     + V 
Sbjct: 561 CSKYTDLLRIALMAEDEAIFEEAHKQVQ 588


>2xzm_Y RPS6E; ribosome, translation; 3.93A {Tetrahymena thermophila} PDB:
           2xzn_Y
          Length = 293

 Score = 27.1 bits (59), Expect = 0.99
 Identities = 17/60 (28%), Positives = 25/60 (41%), Gaps = 4/60 (6%)

Query: 7   RKITPEEMLRKNQRALNKAMRDLDREKQHMEQQE-KKLIADIKKMAKEGQMTLSTERHVA 65
           R ITPE +LRK      K  R     K +  ++E +K +++ KK         S     A
Sbjct: 181 RLITPERILRKKVYKAEKTQR---YVKTNAAKEEYEKFLSEWKKQRAAKAHAASAPVVEA 237


>3lvt_A Glycosyl hydrolase, family 38; PSI, MCSG, structural genomics,
          midwest center for structural genomics, protein
          structure initiative; 2.55A {Enterococcus faecalis}
          Length = 899

 Score = 27.1 bits (59), Expect = 1.4
 Identities = 8/69 (11%), Positives = 20/69 (28%), Gaps = 18/69 (26%)

Query: 1  MEWLFGRKITPEEMLRKNQRALNKAMRDLDREKQH--------------MEQQEKKLIAD 46
           EW        EE   +    ++  +  ++ + +                 Q   +    
Sbjct: 19 REWYL----PYEEHHMRLIELVDNVLDLIENDPEFNSFHLDGQTIILDDYLQVRPEKKEA 74

Query: 47 IKKMAKEGQ 55
          +KK  + G+
Sbjct: 75 VKKAVQAGK 83


>2wyh_A Alpha-mannosidase; hydrolase, glycosidase, glycoside hydrolase;
           1.90A {Streptococcus pyogenes} PDB: 2wyi_A*
          Length = 923

 Score = 26.7 bits (58), Expect = 1.7
 Identities = 5/68 (7%), Positives = 17/68 (25%), Gaps = 18/68 (26%)

Query: 2   EWLFGRKITPEEMLRKNQRALNKAMRDLDREKQH--------------MEQQEKKLIADI 47
           EW        E+   +    ++  +     +                   +   +   +I
Sbjct: 39  EWYM----AYEQHHMRLINLIDDLLEVFQTDPDFHSFHLDGQTIILDDYLKVRPEREPEI 94

Query: 48  KKMAKEGQ 55
           ++    G+
Sbjct: 95  RQAIASGK 102


>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
           vesicle, membrane, Ca structural protein; 7.94A {Bos
           taurus}
          Length = 190

 Score = 25.5 bits (55), Expect = 4.0
 Identities = 10/52 (19%), Positives = 16/52 (30%), Gaps = 6/52 (11%)

Query: 12  EEMLRKNQRALNKAMRDL-DREKQHMEQQEKKLIADIKKMAKEGQMTLSTER 62
                  Q    KA +DL +  ++  EQ EK      K   +        + 
Sbjct: 103 AASKVMEQEWREKAKKDLEEWNQRQSEQVEKN-----KINNRIADKAFYQQP 149


>3g7d_A PHPD; non heme Fe(II) dioxygenase, cupin, biosynthetic protein;
          1.80A {Streptomyces viridochromogenes} PDB: 3gbf_A
          3rzz_A
          Length = 443

 Score = 25.2 bits (54), Expect = 6.1
 Identities = 9/47 (19%), Positives = 15/47 (31%)

Query: 1  MEWLFGRKITPEEMLRKNQRALNKAMRDLDREKQHMEQQEKKLIADI 47
            W+  RK T  +        L+   R L  E    +      +A+ 
Sbjct: 9  AHWMNARKYTAAQTADLAGLPLDDLRRLLGDEANEPDPAAATALAEA 55


>3ac6_A Phosphoribosylformylglycinamidine synthase 2; purine metabolism,
           ATP-binding, ligase, nucleotide-binding, biosynthesis;
           HET: ADP; 2.35A {Thermus thermophilus} PDB: 3viu_A*
          Length = 725

 Score = 24.9 bits (55), Expect = 7.2
 Identities = 17/99 (17%), Positives = 27/99 (27%), Gaps = 27/99 (27%)

Query: 28  DLDREKQHMEQ----QEKKLIADIK------------KMAKEGQM----TLSTERHVALL 67
           DL REK   E      ++ L                 +M     +     +  E   AL 
Sbjct: 595 DLGREKAVQEAIRDLIQRGLTRTAHDVAEGGLLLALAEMTFPYGVGATVEVREEGLEALF 654

Query: 68  LE----FVIIVGPENRENFENSDLRPQSNFFAVFTIGEV 102
            E     +  V     +      L  +   + V  +GE 
Sbjct: 655 GEAPSRVLFTVEKTRLQEATLL-LEERGLPYRV--LGET 690


  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    0.134    0.368 

Gapped
Lambda     K      H
   0.267   0.0601    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,574,159
Number of extensions: 82846
Number of successful extensions: 359
Number of sequences better than 10.0: 1
Number of HSP's gapped: 352
Number of HSP's successfully gapped: 49
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
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 (23.7 bits)