RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 043842
         (129 letters)



>3r8s_C 50S ribosomal protein L2; protein biosynthesis, RNA, tRNA, transfer
           RNA, 23S ribosomal subunit, ribosome recycling factor,
           RRF, ribosome; 3.00A {Escherichia coli} PDB: 3fik_C
           2wwq_C 3oat_C* 3oas_C* 3ofd_C 3ofc_C 3ofr_C* 3ofz_C*
           3og0_C 3ofq_C 3r8t_C 3i1n_C 1vs8_C 1vs6_C 2aw4_C 2awb_C
           2vhm_C 2vhn_C 3bbx_C 3df2_C ...
          Length = 271

 Score =  101 bits (254), Expect = 1e-27
 Identities = 37/86 (43%), Positives = 45/86 (52%), Gaps = 2/86 (2%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRSWLGRRAVVRGVAMIPVD 100
            Y  +RLR G  + ++  CRAT+G V N  H  + L KAG   W G R  VRG AM PVD
Sbjct: 169 AYVTLRLRSGEMRKVEADCRATLGEVGNAEHMLRVLGKAGAARWRGVRPTVRGTAMNPVD 228

Query: 101 HPHVERSKSSGNNGRCSFTPWGKPCK 126
           HPH      +   G+   TPWG   K
Sbjct: 229 HPHGGGEGRNF--GKHPVTPWGVQTK 252


>3v2d_D 50S ribosomal protein L2; ribosome associated inhibitor A, RAIA,
           protein Y, stress RES stationary phase, ribosome
           hibernation, ribosome; 2.70A {Thermus thermophilus} PDB:
           1vsp_B 2hgj_D 2hgq_D 2hgu_D 1vsa_B 2j03_D 2jl6_D 2jl8_D
           2v47_D 2v49_D 2wdi_D 2wdj_D 2wdl_D 2wdn_D 2wh2_D 2wh4_D
           2wrj_D 2wrl_D 2wro_D 2wrr_D ...
          Length = 276

 Score = 98.3 bits (246), Expect = 2e-26
 Identities = 38/89 (42%), Positives = 46/89 (51%), Gaps = 7/89 (7%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRSWLGRRAVVRGVAMIPVD 100
            Y ++RL  G  + +   C AT+G V N  H    L KAG+  WLGRR  VRG AM PVD
Sbjct: 171 DYVILRLPSGELRKVHGECYATVGAVGNADHKNIVLGKAGRSRWLGRRPHVRGAAMNPVD 230

Query: 101 HPHV---ERSKSSGNNGRCSFTPWGKPCK 126
           HPH     R+      GR   +PWG   K
Sbjct: 231 HPHGGGEGRAPR----GRPPASPWGWQTK 255


>3bbo_E Ribosomal protein L2; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 269

 Score = 97.6 bits (244), Expect = 4e-26
 Identities = 37/92 (40%), Positives = 47/92 (51%), Gaps = 12/92 (13%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRSWLGRRAVVRGVAMIPVD 100
           +   ++L  G  ++I   C AT+G V N     K+L +AG + WLG+R VVRGV M PVD
Sbjct: 166 KSATLKLPSGEVRLISKNCSATVGQVGNVGVNQKRLGRAGSKRWLGKRPVVRGVVMNPVD 225

Query: 101 HPHVERSKSSGNNGRCS------FTPWGKPCK 126
           HPH       G  GR         TPWG P  
Sbjct: 226 HPH------GGGEGRAPIGRKSPTTPWGYPAL 251


>1vq8_A 50S ribosomal protein L2P; ribosome 50S, protein-protein complex,
           RNA-RNA complex, PROT complex, peptidyl transferase
           reaction; HET: 1MA OMU OMG UR3 PSU SPS; 2.20A
           {Haloarcula marismortui} SCOP: b.34.5.3 b.40.4.5 PDB:
           1vq4_A* 1vq5_A* 1vq6_A* 1vq7_A* 1s72_A* 1vq9_A* 1vqk_A*
           1vql_A* 1vqm_A* 1vqn_A* 1vqo_A* 1vqp_A* 1yhq_A* 1yi2_A*
           1yij_A* 1yit_A* 1yj9_A* 1yjn_A* 1yjw_A* 2otj_A* ...
          Length = 240

 Score = 91.8 bits (229), Expect = 3e-24
 Identities = 29/96 (30%), Positives = 39/96 (40%), Gaps = 16/96 (16%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRSWLGRRA-----VVRGVA 95
              +V+L  G  K +DP+CRATIG V+      K   KAG +    +        VRGVA
Sbjct: 135 NVAVVKLPSGEMKRLDPQCRATIGVVAGGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVA 194

Query: 96  MIPVDHPHVERSKSSGNNGRCS-----FTPWGKPCK 126
           M  VDHP        G   +        +    P +
Sbjct: 195 MNAVDHPF------GGGGRQHPGKPKSISRNAPPGR 224


>4a17_A RPL8; eukaryotic ribosome, ribosome, eukaryotic initiation factor
           60S, translation, large ribosomal subunit; 3.52A
           {Tetrahymena thermophila} PDB: 4a1a_A 4a1c_A 4a1e_A
          Length = 264

 Score = 90.4 bits (225), Expect = 2e-23
 Identities = 30/96 (31%), Positives = 37/96 (38%), Gaps = 16/96 (16%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAG-----QRSWLGRRAVVRGVA 95
               +RL  G  K I   CRAT+G V+      K + KAG               VRGVA
Sbjct: 145 DKTRIRLPSGARKTIPGSCRATVGIVAGGGRTDKPILKAGNQFHKYARKRKSWPRVRGVA 204

Query: 96  MIPVDHPHVERSKSSGNNGRCS-----FTPWGKPCK 126
           M PVDHPH       G N +        + W    +
Sbjct: 205 MNPVDHPH------GGGNHQHIGHPATVSKWASAGQ 234


>3iz5_B 60S ribosomal protein L2 (L2P); eukaryotic ribosome,homology
           modeling,de novo modeling,ribos proteins,novel ribosomal
           proteins, ribosome; 5.50A {Triticum aestivum} PDB:
           3izr_B 2zkr_a
          Length = 261

 Score = 89.2 bits (222), Expect = 6e-23
 Identities = 28/98 (28%), Positives = 41/98 (41%), Gaps = 7/98 (7%)

Query: 36  KEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAG--QRSWLGRRAV--- 90
             P +    ++L  G +K++   CRA IG V+      K + KAG     +  +R     
Sbjct: 139 HNPDNGTSRIKLPSGAKKIVPSSCRAMIGQVAGGGRTEKPMLKAGNAYHKYRVKRNCWPK 198

Query: 91  VRGVAMIPVDHPH--VERSKSSGNNGRCSFTPWGKPCK 126
           VRGVAM PV+HPH           +      P G+   
Sbjct: 199 VRGVAMNPVEHPHGGGNHQHIGHASTVRRDAPPGQKVG 236


>1giy_D 50S ribosomal protein L2; ribosome assembly, protein synthesis,
           LIFE; 5.50A {Thermus thermophilus} SCOP: i.1.1.1 PDB:
           1ml5_d* 1yl3_D 2b66_D 2b9n_D 2b9p_D
          Length = 178

 Score = 86.4 bits (215), Expect = 1e-22
 Identities = 27/68 (39%), Positives = 35/68 (51%), Gaps = 5/68 (7%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAGQRSWLGRRAV-----VRGVA 95
           +Y +VRL  G  ++I  +CRAT+G V N     K   KAG +    +        VRGVA
Sbjct: 110 KYVIVRLASGEVRMILGKCRATVGEVGNGGRTDKPFVKAGNKHHKMKARGTKWPNVRGVA 169

Query: 96  MIPVDHPH 103
           M  VDHP 
Sbjct: 170 MNAVDHPF 177


>3jyw_B 60S ribosomal protein L2; eukaryotic ribosome, RACK1 protein,
           flexible fitting; 8.90A {Thermomyces lanuginosus} PDB:
           3izc_B 3izs_B 3o58_B 3o5h_B 3u5e_A 3u5i_A 1s1i_B
          Length = 243

 Score = 86.9 bits (216), Expect = 3e-22
 Identities = 31/101 (30%), Positives = 39/101 (38%), Gaps = 16/101 (15%)

Query: 36  KEPTSRYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAG---QRSWLGRRA--V 90
             P      VRL  G +KVI    R  IG ++      K L KAG    +  L R +   
Sbjct: 138 HNPDENKTRVRLPSGAKKVISSDARGVIGVIAGGGRVDKPLLKAGRAFHKYRLKRNSWPK 197

Query: 91  VRGVAMIPVDHPHVERSKSSGNNGRCS-----FTPWGKPCK 126
            RGVAM PVDHPH       G N +        +      +
Sbjct: 198 TRGVAMNPVDHPH------GGGNHQHIGKASTISRGAVSGQ 232


>2ftc_B Mitochondrial ribosomal protein L2; mitochondrial ribosome, large
           ribosomal subunit, ribosomal R ribosome; 12.10A {Bos
           taurus} PDB: 3iy9_B
          Length = 136

 Score = 50.3 bits (121), Expect = 3e-09
 Identities = 12/40 (30%), Positives = 20/40 (50%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSNPSHGAKKLSKAG 80
              +++L    +  +   C AT+G VSN  H  + + KAG
Sbjct: 97  GTAIIQLPSKRQMQVLETCVATVGRVSNVDHNKRVIGKAG 136


>1rl2_A Protein (ribosomal protein L2); RNA-binding domain,
           peptidyltransferease center, X-RAY diffraction; 2.30A
           {Geobacillus stearothermophilus} SCOP: b.34.5.3 b.40.4.5
           PDB: 1c04_A 487d_I
          Length = 137

 Score = 38.2 bits (90), Expect = 1e-04
 Identities = 13/28 (46%), Positives = 19/28 (67%)

Query: 41  RYCLVRLRCGNEKVIDPRCRATIGTVSN 68
           +Y +VRL  G  ++I  +CRAT+G V N
Sbjct: 110 KYVIVRLASGEVRMILGKCRATVGEVGN 137


>2cs4_A Protein C12ORF2; GTP binding, ubiquitin fold, structural
          genomics, NPPSFA, national project on protein
          structural and functional analyses; NMR {Homo sapiens}
          SCOP: d.15.1.5
          Length = 95

 Score = 27.2 bits (60), Expect = 0.85
 Identities = 8/39 (20%), Positives = 16/39 (41%), Gaps = 2/39 (5%)

Query: 24 SSSCRDVNQDFEKE--PTSRYCLVRLRCGNEKVIDPRCR 60
           ++C++V     +    T RY L+      E+ + P   
Sbjct: 27 VTTCQEVVIALAQAIGRTGRYTLIEKWRDTERHLAPHEN 65


>3g7q_A Valine-pyruvate aminotransferase; NP_462565.1, structur genomics,
           joint center for structural genomics, JCSG, prote
           structure initiative; HET: MSE; 1.80A {Salmonella
           typhimurium}
          Length = 417

 Score = 26.5 bits (59), Expect = 3.1
 Identities = 10/40 (25%), Positives = 18/40 (45%), Gaps = 3/40 (7%)

Query: 84  WLGRRAVVRGVAMIPVD--HPHVERSKSSGNNG-RCSFTP 120
            L +R   RGV M+P     P +++     +   R ++ P
Sbjct: 355 LLYQRLKARGVLMVPGHYFFPGLDKPWPHTHQCMRMNYVP 394


>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 = 25.6 bits (55), Expect = 6.3
 Identities = 6/23 (26%), Positives = 10/23 (43%)

Query: 14  LRVQPSRWEASSSCRDVNQDFEK 36
           +R   + W AS S  +  Q  + 
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKF 529


>2k75_A Uncharacterized protein TA0387; closed beta barrel, OB fold,
           structural genomics, PSI-2, protein structure
           initiative; NMR {Thermoplasma acidophilum}
          Length = 106

 Score = 24.8 bits (54), Expect = 6.7
 Identities = 3/15 (20%), Positives = 6/15 (40%)

Query: 114 GRCSFTPWGKPCKSG 128
            R   + +GK  +  
Sbjct: 49  ARIRISSFGKQLQDS 63


  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    0.133    0.438 

Gapped
Lambda     K      H
   0.267   0.0774    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,041,268
Number of extensions: 105435
Number of successful extensions: 168
Number of sequences better than 10.0: 1
Number of HSP's gapped: 156
Number of HSP's successfully gapped: 16
Length of query: 129
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,384,350
Effective search space: 201680100
Effective search space used: 201680100
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: 52 (23.7 bits)