RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2844
         (100 letters)



>4a18_U RPL13, 60S ribosomal protein L36; ribosome, eukaryotic initiation
           factor 6, EIF6, transla large ribosomal subunit, rRNA;
           3.52A {Tetrahymena thermophila} PDB: 4a19_U 4a1b_U
           4a1d_U
          Length = 206

 Score = 82.5 bits (203), Expect = 3e-21
 Identities = 30/98 (30%), Positives = 47/98 (47%), Gaps = 1/98 (1%)

Query: 2   ESLQLNIQRLKEYKSKLIVFPRREKK-KLRKGEATPEERKVATQLKGPLMPIRQSKPKSK 60
           ESL+LN +RL  Y SKL++FPR + K K      T +    A       +P+     + K
Sbjct: 105 ESLELNKKRLLAYVSKLVLFPRHQGKAKKGLVNDTADTSSAAQNALQTSVPLPSVSKREK 164

Query: 61  ARIPSEAEKKFSAFQTLRMARADAKLVGIREKKAREAA 98
           A       +K   ++ +R  + + K  G R+ KA+ AA
Sbjct: 165 AVSNIAELRKKKVYRIIRQEKTNQKWDGKRKAKAQAAA 202


>3u5e_L 60S ribosomal protein L13-A, 60S ribosomal protein L11-A;
           translation, ribosome, ribosomal R ribosomal protein,
           STM1, eukaryotic ribosome; 3.00A {Saccharomyces
           cerevisiae} PDB: 3u5i_L
          Length = 199

 Score = 63.2 bits (153), Expect = 6e-14
 Identities = 39/97 (40%), Positives = 49/97 (50%), Gaps = 12/97 (12%)

Query: 2   ESLQLNIQRLKEYKSKLIVFPRREKKKLRKGEATPEERKVATQLKGPLMPIRQSKPKSKA 61
           E    N+QRLKEY+SK+IVFPR  K                        PI Q     +A
Sbjct: 107 EIFDANVQRLKEYQSKIIVFPRNGKAP----------EAEQVLSAAATFPIAQPATDVEA 156

Query: 62  RIPSEAEKKFSAFQTLRMARADAKLVGIREKKAREAA 98
           R   +     SAF+TLR+AR++ K  GIREK+ARE A
Sbjct: 157 RAVQD--NGESAFRTLRLARSEKKFRGIREKRAREKA 191


>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 = 29.8 bits (66), Expect = 0.12
 Identities = 20/111 (18%), Positives = 32/111 (28%), Gaps = 31/111 (27%)

Query: 2   ESLQLNIQRL---KEYKSKLIVFPR--REKKKLRKGEA---------TPEERKVATQLKG 47
            S+Q  ++RL   K Y++ L+V     +  K      A         T   ++V   L  
Sbjct: 228 HSIQAELRRLLKSKPYENCLLVL-LNVQNAKAW---NAFNLSCKILLTTRFKQVTDFLSA 283

Query: 48  PLMPIRQSKPKSKARIPSEAEKKFSAFQTLRMARADAKLVGIREKK-AREA 97
                      S    P E +                K +  R +   RE 
Sbjct: 284 ATTTHISLDHHSMTLTPDEVKSLL------------LKYLDCRPQDLPREV 322



 Score = 28.3 bits (62), Expect = 0.42
 Identities = 16/71 (22%), Positives = 24/71 (33%), Gaps = 9/71 (12%)

Query: 1   MESLQLNIQRLKEYKSKLIVFPRREK---KKLRK--GEATPEE-RKVATQLKGPLMPIRQ 54
           +  L+    R K +   L VFP         L     +    +   V  +L    +  +Q
Sbjct: 363 LNVLEPAEYR-KMFDR-LSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ 420

Query: 55  SKPKSKARIPS 65
            K  S   IPS
Sbjct: 421 PKE-STISIPS 430


>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 = 27.6 bits (60), Expect = 0.63
 Identities = 7/36 (19%), Positives = 15/36 (41%), Gaps = 13/36 (36%)

Query: 25 EKKKLRKGEAT-----PEERKVATQLKGPLMPIRQS 55
          EK+ L+K +A+      +          P + I+ +
Sbjct: 18 EKQALKKLQASLKLYADDS--------APALAIKAT 45


>2zuv_A Lacto-N-biose phosphorylase; beta-alpha-barrel, TIM barrel,
           glycosyltransferase, transferase; HET: NDG; 1.85A
           {Bifidobacterium longum} PDB: 2zus_A* 2zuu_A* 2zut_A*
           2zuw_A*
          Length = 759

 Score = 27.2 bits (60), Expect = 0.92
 Identities = 8/46 (17%), Positives = 19/46 (41%)

Query: 52  IRQSKPKSKARIPSEAEKKFSAFQTLRMARADAKLVGIREKKAREA 97
           +      S  R+P +A++ +  F +  +     +L  +     +EA
Sbjct: 262 VDGGAYNSAWRVPRKAQRDWIDFLSGFVRENVKQLADMSHAAGKEA 307


>2b0a_A Hypothetical protein MJ0783; structural genomics, PSI, protein STRU
           initiative; 1.45A {Methanocaldococcus jannaschii} SCOP:
           c.8.8.1
          Length = 186

 Score = 26.7 bits (59), Expect = 1.3
 Identities = 8/36 (22%), Positives = 16/36 (44%), Gaps = 4/36 (11%)

Query: 1   MESLQLNIQRLKEYKSKLIVFPRREKKKLRKGEATP 36
           +E+L  N++ L       +  P     K+   +A+P
Sbjct: 147 IENLNENLKNLVGKSFYFLGLPL----KIFDIDASP 178


>2wsi_A FAD synthetase; transferase, nucleotidyltransferase,
           nucleotide-binding; HET: FAD; 1.90A {Saccharomyces
           cerevisiae}
          Length = 306

 Score = 26.0 bits (56), Expect = 2.3
 Identities = 10/63 (15%), Positives = 24/63 (38%)

Query: 2   ESLQLNIQRLKEYKSKLIVFPRREKKKLRKGEATPEERKVATQLKGPLMPIRQSKPKSKA 61
                 ++  + Y   L    R+    +   +A  +  K+  + +  ++ IR + P  +A
Sbjct: 115 TLENFVLETSERYCLSLYESQRQSGASVNMADAFRDFIKIYPETEAIVIGIRHTDPFGEA 174

Query: 62  RIP 64
             P
Sbjct: 175 LKP 177


>2o1s_A 1-deoxy-D-xylulose-5-phosphate synthase; DXS, thiamine, isoprenoid,
           transferase; HET: TDP; 2.40A {Escherichia coli}
          Length = 621

 Score = 24.4 bits (54), Expect = 8.9
 Identities = 14/46 (30%), Positives = 17/46 (36%), Gaps = 8/46 (17%)

Query: 47  GPLMPIRQSKPKSKARIPSEAEKKFSA-F-QTL-RMARADAKLVGI 89
               P     PKS   +PS     +S  F   L   A  D KL+ I
Sbjct: 302 PKFDPSSGCLPKSSGGLPS-----YSKIFGDWLCETAAKDNKLMAI 342


  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
   0.313    0.128    0.333 

Gapped
Lambda     K      H
   0.267   0.0539    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,384,710
Number of extensions: 69481
Number of successful extensions: 128
Number of sequences better than 10.0: 1
Number of HSP's gapped: 124
Number of HSP's successfully gapped: 26
Length of query: 100
Length of database: 6,701,793
Length adjustment: 66
Effective length of query: 34
Effective length of database: 4,859,007
Effective search space: 165206238
Effective search space used: 165206238
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 (23.9 bits)