RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 032454
         (140 letters)



>3r8s_N 50S ribosomal protein L17; protein biosynthesis, RNA, tRNA,
           transfer RNA, 23S ribosomal subunit, ribosome recycling
           factor, RRF, ribosome; 3.00A {Escherichia coli} PDB:
           3fik_N 2wwq_N 3oat_N* 3oas_N* 3ofd_N 3ofc_N 3ofr_N*
           3ofz_N* 3og0_N 3ofq_N 3r8t_N 3i1n_N 1p85_L 1p86_L 1vs8_N
           1vs6_N 2aw4_N 2awb_N 1vt2_N 2i2v_N ...
          Length = 120

 Score =  146 bits (372), Expect = 5e-47
 Identities = 48/95 (50%), Positives = 64/95 (67%)

Query: 1   MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
           M   LV+HE I+TT+ KAKE+RR+ + ++ L K  S+   R A A  R ++++ KLF EL
Sbjct: 24  MAGSLVRHEIIKTTLPKAKELRRVVEPLITLAKTDSVANRRLAFARTRDNEIVAKLFNEL 83

Query: 61  AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVDR 95
             R+  RAGGYTR+L+   R GD APMAYIE VDR
Sbjct: 84  GPRFASRAGGYTRILKCGFRAGDNAPMAYIELVDR 118


>2cqm_A Ribosomal protein L17 isolog; alpha and beta (A+B), structural
           genomics, NPPSFA, national project on protein structural
           and functional analyses; NMR {Homo sapiens} SCOP:
           d.188.1.1 PDB: 2ftc_J 3iy9_S
          Length = 122

 Score =  142 bits (360), Expect = 5e-45
 Identities = 40/98 (40%), Positives = 56/98 (57%), Gaps = 2/98 (2%)

Query: 1   MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCA--ARRAAAFVRGDDVIHKLFT 58
           +++ LV+HERIE   A+  E+R  A+ ++  GK G       R A  ++   D+I KLF 
Sbjct: 12  LLTGLVRHERIEAPWARVDEMRGYAEKLIDYGKLGDTNERAMRMADFWLTEKDLIPKLFQ 71

Query: 59  ELAYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFVDRE 96
            LA RYKD+ GGYTR+L+   R  D A MA IE+    
Sbjct: 72  VLAPRYKDQTGGYTRMLQIPNRSLDRAKMAVIEYKGNC 109


>2zjr_K 50S ribosomal protein L17; ribosome, large ribosomal subunit,
           ribonucleoprotein, RNA-binding, rRNA-binding,
           tRNA-binding, methylation; 2.91A {Deinococcus
           radiodurans} SCOP: d.188.1.1 PDB: 1nwx_L* 1nwy_L*
           1sm1_L* 1xbp_L* 2zjp_K* 2zjq_K 1nkw_L 3cf5_K* 3dll_K*
           3pio_K* 3pip_K* 1pnu_L 1pny_L 1vor_O 1vou_O 1vow_O
           1voy_O 1vp0_O
          Length = 116

 Score =  135 bits (343), Expect = 1e-42
 Identities = 37/93 (39%), Positives = 54/93 (58%)

Query: 1   MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
             + L++  RI+TT+ KAKE+R   + ++   K G L + R  A  +   DV+ K+  E+
Sbjct: 24  QATALLREGRIQTTLTKAKELRPFVEQLITTAKGGDLHSRRLVAQDIHDKDVVRKVMDEV 83

Query: 61  AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 93
           A +Y +R GGYTR+LR   R GD   MA IE V
Sbjct: 84  APKYAERPGGYTRILRVGTRRGDGVTMALIELV 116


>1gd8_A 50S ribosomal protein L17; two domains, ribosomal protein S8-like
           domain, Trp repressor-like domain, helix-turn-helix
           motif; 2.30A {Thermus thermophilus} SCOP: d.188.1.1 PDB:
           1vsa_L 1vsp_L 1yl3_0 2b66_R 2b9n_R 2b9p_R 2hgj_Q 2hgq_Q
           2hgu_Q 2j01_R 2j03_R 2jl6_R 2jl8_R 2v47_R 2v49_R 2wdi_R
           2wdj_R 2wdl_R 2wdn_R 2wh2_R ...
          Length = 118

 Score =  135 bits (342), Expect = 2e-42
 Identities = 42/95 (44%), Positives = 58/95 (61%), Gaps = 1/95 (1%)

Query: 1   MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
               L+ H RI TTV KAKE+R   D+++ L K G L A R     ++   ++ KLF E+
Sbjct: 24  QAKSLLTHGRITTTVPKAKELRGFVDHLIHLAKRGDLHARRLVLRDLQDVKLVRKLFDEI 83

Query: 61  AYRYKDRAGGYTRLLRS-RIRVGDAAPMAYIEFVD 94
           A RY+DR GGYTR+L+    R GD AP+A +E V+
Sbjct: 84  APRYRDRQGGYTRVLKLAERRRGDGAPLALVELVE 118


>3bbo_P Ribosomal protein L17; large ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea} SCOP: i.1.1.2
          Length = 205

 Score =  135 bits (342), Expect = 2e-41
 Identities = 45/93 (48%), Positives = 64/93 (68%)

Query: 1   MVSQLVKHERIETTVAKAKEVRRLADNMVQLGKEGSLCAARRAAAFVRGDDVIHKLFTEL 60
           + +QL+KH RI+TT A+A+ VR+  D M+ + K+GSL   R+A  F+    ++H LF E+
Sbjct: 113 LTTQLLKHGRIKTTKARARAVRKYVDKMITMAKDGSLHKRRQALGFIYEKQIVHALFAEV 172

Query: 61  AYRYKDRAGGYTRLLRSRIRVGDAAPMAYIEFV 93
             RY +R GGYTR++R+  R GD APMAYIE V
Sbjct: 173 PDRYGERNGGYTRIIRTLPRRGDNAPMAYIELV 205


>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 = 26.9 bits (59), Expect = 2.6
 Identities = 23/139 (16%), Positives = 41/139 (29%), Gaps = 35/139 (25%)

Query: 2   VSQLVKHERIETTVAKAKEV-------RRLADNMVQLGKEGSL--CAARRAAAFV----- 47
            ++L++    +TT+ K KE+       R +A          +L        A  V     
Sbjct: 105 AAKLLQEN--DTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGG 162

Query: 48  RGDDVIHKLFTELAYRYK----------DRAGGYTRLLRSRIRVGDAAPMAYIEFVDREN 97
           +G+      F EL   Y+            +      L   IR    A   + + ++   
Sbjct: 163 QGN--TDDYFEELRDLYQTYHVLVGDLIKFSA---ETLSELIRTTLDAEKVFTQGLNILE 217

Query: 98  ELRQSKPAVPQPPPRAALD 116
            L          P +  L 
Sbjct: 218 WLENPSNT----PDKDYLL 232


>3h11_B Caspase-8; cell death, apoptosis, caspase, alternative splicing,
           HOST- virus interaction, polymorphism, cytoplasm,
           disease mutation; 1.90A {Homo sapiens} PDB: 2k7z_A
           1i4e_B 2fun_B 2c2z_B*
          Length = 271

 Score = 26.7 bits (58), Expect = 2.7
 Identities = 5/22 (22%), Positives = 5/22 (22%), Gaps = 1/22 (4%)

Query: 117 PWTRSRLTKNFA-PPKQEKSSD 137
           P     L K    P   E    
Sbjct: 248 PQPTFTLRKKLVFPSDVEHHHH 269


>2qzs_A Glycogen synthase; glycosyl-transferase, GT-B fold, rossmann fold,
           closed-form, ADP and glucose binding, glycogen
           biosynthesis; HET: GLC ADP 250; 2.20A {Escherichia coli}
           PDB: 2r4t_A* 2r4u_A* 3guh_A* 3cx4_A* 3cop_A* 3d1j_A
          Length = 485

 Score = 26.7 bits (60), Expect = 3.2
 Identities = 7/23 (30%), Positives = 10/23 (43%)

Query: 49  GDDVIHKLFTELAYRYKDRAGGY 71
           GD V+ + F   A  Y  + G  
Sbjct: 330 GDPVLQEGFLAAAAEYPGQVGVQ 352


>1rzu_A Glycogen synthase 1; glycosyl-transferase, GT-B fold, rossmann
           fold, ADP-binding, transferase; HET: ADP; 2.30A
           {Agrobacterium tumefaciens} SCOP: c.87.1.8 PDB: 1rzv_A
          Length = 485

 Score = 26.4 bits (59), Expect = 3.7
 Identities = 6/23 (26%), Positives = 8/23 (34%)

Query: 49  GDDVIHKLFTELAYRYKDRAGGY 71
           GD  +       A R+  R G  
Sbjct: 329 GDVALEGALLAAASRHHGRVGVA 351


>2abw_A PDX2 protein, glutaminase; PLP-synthase, vitamin B6, malaria,
           transferase; HET: PG4; 1.62A {Plasmodium falciparum}
           SCOP: c.23.16.1 PDB: 4ads_G
          Length = 227

 Score = 26.2 bits (57), Expect = 4.4
 Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 9/62 (14%)

Query: 11  IETTVAKAKEVRRLADNMVQLGKEGSLCAARR----AAAF---VRGDDVIHKLFTELAYR 63
           I   ++   +V  LA    +      + A  +       F   +       + F E    
Sbjct: 158 IREILSDEVKV--LATFSHESYGPNIIAAVEQNNCLGTVFHPELLPHTAFQQYFYEKVKN 215

Query: 64  YK 65
           YK
Sbjct: 216 YK 217


  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
   0.318    0.132    0.379 

Gapped
Lambda     K      H
   0.267   0.0844    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,154,532
Number of extensions: 127533
Number of successful extensions: 416
Number of sequences better than 10.0: 1
Number of HSP's gapped: 414
Number of HSP's successfully gapped: 16
Length of query: 140
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 56
Effective length of database: 4,356,429
Effective search space: 243960024
Effective search space used: 243960024
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 (23.6 bits)