RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 044569
         (116 letters)



>3r8s_T 50S ribosomal protein L23; protein biosynthesis, RNA, tRNA,
           transfer RNA, 23S ribosomal subunit, ribosome recycling
           factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
           3fik_T 2wwq_T 3oat_T* 3oas_T* 3ofd_T 3ofc_T 3ofr_T*
           3ofz_T* 3og0_T 3ofq_T 3r8t_T 2j28_T 3e1b_M 3e1d_M 3iy9_T
           3i1n_T 1p85_R 1p86_R 1vs8_T 1vs6_T ...
          Length = 93

 Score = 40.6 bits (96), Expect = 7e-06
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 69  EVDEARTLNKGGKKKKWGGLLNAKPDYKKAYVT 101
           EV+   TL   GK K+ G  +  + D+KKAYVT
Sbjct: 54  EVEVVNTLVVKGKVKRHGQRIGRRSDWKKAYVT 86


>2zjr_Q 50S ribosomal protein L23; ribosome, large ribosomal subunit,
           ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} SCOP: d.12.1.1 PDB: 1sm1_R* 2aar_R 2d3o_R
           2zjp_Q* 2zjq_Q 1nkw_R 3cf5_Q* 3dll_Q* 3pio_Q* 3pip_Q*
           1nwy_R* 1nwx_R* 1xbp_R* 1pnu_R 1pny_R 1vor_U 1vou_U
           1vow_U 1voy_U 1vp0_U
          Length = 95

 Score = 39.1 bits (92), Expect = 2e-05
 Identities = 12/33 (36%), Positives = 17/33 (51%)

Query: 69  EVDEARTLNKGGKKKKWGGLLNAKPDYKKAYVT 101
            V    T+N  GK+K+ G  +  + D KKA V 
Sbjct: 49  RVIGISTMNVPGKRKRVGRFIGQRNDRKKAIVR 81


>3tve_T 50S ribosomal protein L23; RNA, ribosome, tRNA, translation, mRNA;
           3.10A {Thermus thermophilus} PDB: 3pyr_T 3pyo_T 3pyv_T
           3pyt_T 3tvh_T 1n88_A 1vsa_R 1vsp_R 2hgj_W 2hgq_W 2hgu_W
           2j01_X 2j03_X 2jl6_X 2jl8_X 2v47_X 2v49_X 2wdi_X 2wdj_X
           2wdl_X ...
          Length = 92

 Score = 39.0 bits (92), Expect = 2e-05
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 69  EVDEARTLNKGGKKKKWGGLLNAKPDYKKAYVT 101
           +V +  TL+  GKKK+ G  L  +PD KKA V 
Sbjct: 48  KVVKVNTLHVRGKKKRLGRYLGKRPDRKKAIVQ 80


>3l7y_A Putative uncharacterized protein SMU.1108C; hydrolase; 2.00A
           {Streptococcus mutans}
          Length = 304

 Score = 26.9 bits (60), Expect = 1.7
 Identities = 9/34 (26%), Positives = 13/34 (38%), Gaps = 7/34 (20%)

Query: 48  MPNTFQNIKEIAAKTIPSNGFEVDE---ARTLNK 78
           M N  +N+K  A     SN    DE      ++ 
Sbjct: 269 MANAPKNVKAAANYQAKSN----DESGVLDVIDN 298


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

 Score = 25.9 bits (56), Expect = 2.9
 Identities = 15/72 (20%), Positives = 26/72 (36%), Gaps = 7/72 (9%)

Query: 2   ARTAPEKTEAQNTERERRSTEWEIRSEITEAQNGKQAAGNLPIKLLMPNTFQNIKEIAAK 61
               PE       E+ +R  E +  S++ E +  ++A  +L          Q   E   K
Sbjct: 80  LTQEPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDL------EEWNQRQSEQVEK 133

Query: 62  TIPSNGFEVDEA 73
              +N    D+A
Sbjct: 134 NKINNR-IADKA 144


>1rlm_A Phosphatase; HAD family, rossman fold, hydrolase; 1.90A
           {Escherichia coli} SCOP: c.108.1.10 PDB: 1rlt_A 1rlo_A*
           2hf2_A
          Length = 271

 Score = 26.0 bits (58), Expect = 3.1
 Identities = 8/34 (23%), Positives = 12/34 (35%), Gaps = 7/34 (20%)

Query: 48  MPNTFQNIKEIAAKTIPSNGFEVDE---ARTLNK 78
           M N  +NIK+IA      N    +       +  
Sbjct: 232 MGNAAENIKQIARYATDDN----NHEGALNVIQA 261


>3dao_A Putative phosphatse; structural genomics, joint center for S
           genomics, JCSG, protein structure initiative, PSI-2,
           hydrol; HET: MSE 1PE CIT; 1.80A {Eubacterium rectale}
          Length = 283

 Score = 25.6 bits (57), Expect = 3.8
 Identities = 6/34 (17%), Positives = 8/34 (23%), Gaps = 7/34 (20%)

Query: 48  MPNTFQNIKEIAAKTIPSNGFEVDE---ARTLNK 78
           + N  Q +   A  T         E      L  
Sbjct: 252 VSNARQEVIAAAKHTCAPY----WENGVLSVLKS 281


>3luf_A Two-component system response regulator/ggdef domain protein;
           structural genomics, ASA_2441, PSI-2, protein structure
           initiative; HET: MSE; 1.76A {Aeromonas salmonicida} PDB:
           3mf4_A*
          Length = 259

 Score = 25.7 bits (57), Expect = 4.1
 Identities = 11/72 (15%), Positives = 28/72 (38%), Gaps = 20/72 (27%)

Query: 28  EITEAQNGKQA----AGNLPIKLL-----MP--NTFQNIKEI----AAKTIP-----SNG 67
           ++ EA + ++A      +  I+L+     MP  +    ++ +    + + +       + 
Sbjct: 150 QVHEASHAREALATLEQHPAIRLVLVDYYMPEIDGISLVRMLRERYSKQQLAIIGISVSD 209

Query: 68  FEVDEARTLNKG 79
                AR L +G
Sbjct: 210 KRGLSARYLKQG 221


>2ucz_A UBC7, ubiquitin conjugating enzyme; ubiquitin conjugation, ligase,
           yeast; 2.93A {Saccharomyces cerevisiae} SCOP: d.20.1.1
          Length = 165

 Score = 25.4 bits (56), Expect = 4.7
 Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 10/40 (25%)

Query: 86  GGLLNAKPDYKKAYVTSPPRTRFRC----------GRICL 115
            G+ NAK ++ K Y  SPP+  F            G +C+
Sbjct: 51  DGVFNAKLEFPKDYPLSPPKLTFTPSILHPNIYPNGEVCI 90


>3h8k_A Ubiquitin-conjugating enzyme E2 G2; alpha beta, all alpha, ligase,
           UBL conjugation pathway, endo reticulum, membrane,
           metal-binding; 1.80A {Homo sapiens} PDB: 3fsh_A 2cyx_A
           2kly_A
          Length = 164

 Score = 25.0 bits (55), Expect = 5.4
 Identities = 12/40 (30%), Positives = 17/40 (42%), Gaps = 10/40 (25%)

Query: 86  GGLLNAKPDYKKAYVTSPPRTRFRC----------GRICL 115
            G+  A   +   Y  SPP+ RF C          GR+C+
Sbjct: 50  FGVFPAILSFPLDYPLSPPKMRFTCEMFHPNIYPDGRVCI 89


>2gjd_A Ubiquitin-conjugating enzyme E2-18 kDa; UBC9P, SMT3,
           crystallography, ligase; 1.75A {Saccharomyces
           cerevisiae} PDB: 2eke_A 3ong_B
          Length = 157

 Score = 24.5 bits (54), Expect = 7.9
 Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 10/41 (24%)

Query: 85  WGGLLNAKPDYKKAYVTSPPRTRFRC----------GRICL 115
            GG+     +Y   Y + PP+ +F            G ICL
Sbjct: 54  AGGVYPITVEYPNEYPSKPPKVKFPAGFYHPNVYPSGTICL 94


>3rz3_A Ubiquitin-conjugating enzyme E2 R1; ubiquitin conjugating enzyme
           domain, E2 domain, ligase-ligas inhibitor complex; HET:
           U94; 2.30A {Homo sapiens} PDB: 2ob4_A
          Length = 183

 Score = 24.3 bits (53), Expect = 9.8
 Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 10/40 (25%)

Query: 86  GGLLNAKPDYKKAYVTSPPRTRFRC----------GRICL 115
           GG   A+  +   Y  SPP  RF            G +C+
Sbjct: 54  GGYFKARLKFPIDYPYSPPAFRFLTKMWHPNIYETGDVCI 93


  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    0.129    0.375 

Gapped
Lambda     K      H
   0.267   0.0666    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,687,244
Number of extensions: 87141
Number of successful extensions: 108
Number of sequences better than 10.0: 1
Number of HSP's gapped: 106
Number of HSP's successfully gapped: 17
Length of query: 116
Length of database: 6,701,793
Length adjustment: 79
Effective length of query: 37
Effective length of database: 4,496,034
Effective search space: 166353258
Effective search space used: 166353258
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 (23.6 bits)