RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10549
         (103 letters)



>2hye_C Cullin-4A, CUL-4A; beta propeller, ring finger, zinc finger,
           propeller cluster, helical repeats, cullin repeats,
           protein binding; HET: DNA; 3.10A {Homo sapiens} SCOP:
           a.4.5.34 a.118.17.1 e.40.1.1 PDB: 4a0k_A* 4a0c_C 4a0l_E*
          Length = 759

 Score = 82.2 bits (202), Expect = 6e-20
 Identities = 17/66 (25%), Positives = 32/66 (48%)

Query: 32  TMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTA 91
            + + Y QD W  L  A++ +Q   +   + EELY+    +  HK    LY  L++    
Sbjct: 53  RLPDNYTQDTWRKLHEAVRAVQSSTSIRYNLEELYQAVENLCSHKVSPMLYKQLRQACED 112

Query: 92  HLETKV 97
           H++ ++
Sbjct: 113 HVQAQI 118


>4eoz_B Cullin-3, CUL-3; E3 ubiquitin ligase, nucleus, protein binding;
          2.40A {Homo sapiens} PDB: 4apf_B
          Length = 364

 Score = 77.2 bits (189), Expect = 2e-18
 Identities = 57/67 (85%), Positives = 61/67 (91%)

Query: 31 MTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVT 90
          MTMDEKYV  IW LLKNAIQEIQ+KNNSGLSFEELYRNAYTMVLHKHGE+LY+GL+EVVT
Sbjct: 6  MTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRNAYTMVLHKHGEKLYTGLREVVT 65

Query: 91 AHLETKV 97
           HL  KV
Sbjct: 66 EHLINKV 72


>4a64_A Cullin-4B, CUL4B, CUL-4B; cell cycle; 2.57A {Homo sapiens}
          Length = 354

 Score = 70.3 bits (171), Expect = 6e-16
 Identities = 17/66 (25%), Positives = 33/66 (50%)

Query: 32 TMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLKEVVTA 91
           + E Y  + W  LK A++ IQ   +   + EELY+    +  +K    LY  L+++   
Sbjct: 4  KLPENYTDETWQKLKEAVEAIQNSTSIKYNLEELYQAVENLCSYKISANLYKQLRQICED 63

Query: 92 HLETKV 97
          H++ ++
Sbjct: 64 HIKAQI 69


>4ap2_B Cullin-3, CUL-3; ubiquitination, E3 ligase, cell cycle; HET: EDO;
          2.80A {Homo sapiens} PDB: 4apf_B
          Length = 410

 Score = 69.5 bits (169), Expect = 1e-15
 Identities = 58/71 (81%), Positives = 62/71 (87%)

Query: 27 RDHLMTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFEELYRNAYTMVLHKHGERLYSGLK 86
          R   MTMDEKYV  IW LLKNAIQEIQ+KNNSGLSFEELYRNAYTMVLHKHGE+LY+GL+
Sbjct: 19 RAFPMTMDEKYVNSIWDLLKNAIQEIQRKNNSGLSFEELYRNAYTMVLHKHGEKLYTGLR 78

Query: 87 EVVTAHLETKV 97
          EVVT HL  KV
Sbjct: 79 EVVTEHLINKV 89


>2wzk_A Cullin-5, CUL-5; UBL conjugation pathway, HIV, phosphoprotein,
          isopeptide bond, protein binding; 2.05A {Mus musculus}
          Length = 391

 Score = 54.1 bits (129), Expect = 3e-10
 Identities = 8/62 (12%), Positives = 29/62 (46%), Gaps = 3/62 (4%)

Query: 39 QDIWLLLKNAIQEIQKKNN-SGLSFEELYRNAYTMVL--HKHGERLYSGLKEVVTAHLET 95
          +D W  +   + ++ ++ + +   + +L+ + + + L   K   +++  LKE +   ++ 
Sbjct: 16 EDKWDFMHPIVLKLLRQESVTKQQWFDLFSDVHAVCLWDDKGSSKIHQALKEDILEFIKQ 75

Query: 96 KV 97
            
Sbjct: 76 AQ 77


>1ldj_A Cullin homolog 1, CUL-1; cullin, ROC1, HRT1, zinc ring finger,
          ligase, ubiquitin, ubiquitination, SCF; 3.00A {Homo
          sapiens} SCOP: a.4.5.34 a.118.17.1 e.40.1.1 PDB: 1u6g_A
          1ldk_A 1ldk_B 3rtr_A
          Length = 760

 Score = 49.4 bits (117), Expect = 2e-08
 Identities = 18/86 (20%), Positives = 28/86 (32%), Gaps = 28/86 (32%)

Query: 40 DIWLLLKNAIQEIQKKNNSGLS-FEELYRNAYTMVLHKH--------------------- 77
           IW  L+  IQ++  + +   S + ELY + Y      H                     
Sbjct: 3  QIWDDLRAGIQQVYTRQSMAKSRYMELYTHVYNYCTSVHQSNQARGAGVPPSKSKKGQTP 62

Query: 78 ------GERLYSGLKEVVTAHLETKV 97
                G  LY  LKE +  +L   +
Sbjct: 63 GGAQFVGLELYKRLKEFLKNYLTNLL 88


>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 = 32.3 bits (73), Expect = 0.016
 Identities = 19/95 (20%), Positives = 31/95 (32%), Gaps = 34/95 (35%)

Query: 21   NGHRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQKKNNSGLSFE----ELYRNAYT---MV 73
             G R  R++   M  + + D  L  +   +EI + + S  +F      L    +T   + 
Sbjct: 1680 KGKRI-RENYSAMIFETIVDGKLKTEKIFKEINEHSTS-YTFRSEKGLLSATQFTQPALT 1737

Query: 74   LH--------K-------------H--GERLYSGL 85
            L         K             H  GE  Y+ L
Sbjct: 1738 LMEKAAFEDLKSKGLIPADATFAGHSLGE--YAAL 1770


>2hcf_A Hydrolase, haloacid dehalogenase-like family; NP_662590.1, ST
           genomics, PSI-2, protein structure initiative; 1.80A
           {Chlorobaculum tepidum} SCOP: c.108.1.6
          Length = 234

 Score = 25.8 bits (57), Expect = 2.7
 Identities = 6/30 (20%), Positives = 13/30 (43%)

Query: 62  FEELYRNAYTMVLHKHGERLYSGLKEVVTA 91
            +E Y   +     +    L  G++E++ A
Sbjct: 75  AKETYIALFRERARREDITLLEGVRELLDA 104


>3qa8_A MGC80376 protein; kinase ubiquitin-like domain, phosphorylation,
           kinase domain ubiquitin-like domain, kinase, substrate
           binding; 3.60A {Xenopus laevis} PDB: 3qad_A* 3rzf_A*
          Length = 676

 Score = 25.4 bits (55), Expect = 4.9
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 23  HRTSRDHLMTMDEKYVQDIWLLLKNAIQEIQ 53
            R     ++   EK  Q++W LLK A  +++
Sbjct: 637 MREDEKIVVRRQEKRQQELWNLLKIACSKVR 667


  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
   0.312    0.126    0.343 

Gapped
Lambda     K      H
   0.267   0.0465    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,410,861
Number of extensions: 69505
Number of successful extensions: 118
Number of sequences better than 10.0: 1
Number of HSP's gapped: 115
Number of HSP's successfully gapped: 15
Length of query: 103
Length of database: 6,701,793
Length adjustment: 68
Effective length of query: 35
Effective length of database: 4,803,165
Effective search space: 168110775
Effective search space used: 168110775
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 51 (24.1 bits)