RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 034105
         (103 letters)



>3r8n_N 30S ribosomal protein S14; protein biosynthesis, RNA, tRNA,
           transfer RNA, 16S ribosomal subunit, RRF; 3.00A
           {Escherichia coli} PDB: 1p6g_N 1p87_N 2aw7_N 2avy_N
           2i2u_N 2i2p_N* 2qan_N* 2qb9_N* 2qbb_N* 2qbd_N 2qbf_N
           2qbh_N* 2qbj_N* 2qou_N* 2qow_N* 2qoy_N* 2qp0_N* 2vho_N
           2vhp_N 2ykr_N ...
          Length = 100

 Score =  100 bits (252), Expect = 1e-29
 Identities = 42/92 (45%), Positives = 53/92 (57%)

Query: 12  DHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGR 71
           + KR  LA K+  KR   K++  DVN   E R   + KL  LPR+SS +R RNRC  TGR
Sbjct: 9   EVKRVALADKYFAKRAELKAIISDVNASDEDRWNAVLKLQTLPRDSSPSRQRNRCRQTGR 68

Query: 72  SRAVYEKFRMSRIVFRSLANQGMLMGVKKASW 103
                 KF +SRI  R  A +G + G+KKASW
Sbjct: 69  PHGFLRKFGLSRIKVREAAMRGEIPGLKKASW 100


>3bbn_N Ribosomal protein S14; small ribosomal subunit, spinach chloroplast
           ribosome, ribonucleoprotein particle, macromolecular
           complex; 9.40A {Spinacea oleracea}
          Length = 100

 Score = 98.7 bits (247), Expect = 9e-29
 Identities = 31/92 (33%), Positives = 44/92 (47%), Gaps = 1/92 (1%)

Query: 12  DHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLARLPRNSSFTRLRNRCIFTGR 71
           + KRR L  K+ L R+  K   R        + +   KL   PRNS+  RL  RC  TGR
Sbjct: 10  EKKRRNLEQKYHLIRRSSKQEIRK-VTSLSDKWEIHGKLQSPPRNSAPARLHRRCFLTGR 68

Query: 72  SRAVYEKFRMSRIVFRSLANQGMLMGVKKASW 103
            RA    F +S  + R + +  +L G  ++SW
Sbjct: 69  PRANIRDFGLSGHILREMVHTCLLPGATRSSW 100


>2vqe_N 30S ribosomal protein S14 type Z; tRNA-binding, rRNA-binding,
           metal-binding, zinc-finger, translation; HET: TM2 PAR;
           2.5A {Thermus thermophilus} SCOP: g.39.1.7 PDB: 1gix_Q*
           1hnw_N* 1hnx_N* 1hnz_N* 1hr0_N 1ibk_N* 1ibl_N* 1ibm_N
           1jgo_Q* 1jgp_Q* 1jgq_Q* 1ml5_Q* 1xmo_N* 1xmq_N* 1xnq_N*
           1xnr_N* 1yl4_Q 2b64_N* 2b9m_N* 2b9o_N* ...
          Length = 61

 Score = 74.6 bits (184), Expect = 1e-19
 Identities = 26/61 (42%), Positives = 36/61 (59%), Gaps = 2/61 (3%)

Query: 43  REKYLCKLARLPRNSSFTRLRNRCIFTGRSRAVYEKFRMSRIVFRSLANQGMLMGVKKAS 102
           R+  + K  R P+     R   RC+  GR+R+VY  F + RI  R LA++G L GV+KAS
Sbjct: 3   RKALIEKAKRTPKFK--VRAYTRCVRCGRARSVYRFFGLCRICLRELAHKGQLPGVRKAS 60

Query: 103 W 103
           W
Sbjct: 61  W 61


>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 = 30.2 bits (67), Expect = 0.11
 Identities = 6/28 (21%), Positives = 12/28 (42%), Gaps = 7/28 (25%)

Query: 26  RKLYKSLY---RDVNLPTEVREKYLCKL 50
           RK++  L       ++PT +    L  +
Sbjct: 372 RKMFDRLSVFPPSAHIPTIL----LSLI 395



 Score = 28.3 bits (62), Expect = 0.49
 Identities = 12/85 (14%), Positives = 33/85 (38%), Gaps = 16/85 (18%)

Query: 8   RNIEDHKRRLLATKFELKRKLYKS------LYRDVNL----PTEVREKYLCKLARLPRNS 57
           ++++D  + +L+ + E+   +  S        R          E+ +K++ ++  L  N 
Sbjct: 36  KDVQDMPKSILSKE-EID-HIIMSKDAVSGTLRLFWTLLSKQEEMVQKFVEEV--LRINY 91

Query: 58  SF--TRLRNRCIFTGRSRAVYEKFR 80
            F  + ++           +Y + R
Sbjct: 92  KFLMSPIKTEQRQPSMMTRMYIEQR 116



 Score = 27.9 bits (61), Expect = 0.68
 Identities = 14/56 (25%), Positives = 19/56 (33%), Gaps = 10/56 (17%)

Query: 9   NIEDHKRRLLATKFELKRKLYK-SLY--RDVNLPTEVRE-KYLCKLARLPRNSSFT 60
           +I+   RRL      LK K Y+  L    +V            CK+    R    T
Sbjct: 229 SIQAELRRL------LKSKPYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVT 278



 Score = 24.8 bits (53), Expect = 6.8
 Identities = 13/91 (14%), Positives = 29/91 (31%), Gaps = 12/91 (13%)

Query: 11  EDHKRRLLATKFELKRKLYKSLYRDVNLPTE--------VREKYLCKLARLPRNSSFTRL 62
           + HK  L+  + +       S+Y ++ +  E        + + Y         +     L
Sbjct: 410 KLHKYSLVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYL 469

Query: 63  RN-RCIFTG---RSRAVYEKFRMSRIVFRSL 89
                   G   ++    E+  + R+VF   
Sbjct: 470 DQYFYSHIGHHLKNIEHPERMTLFRMVFLDF 500


>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 = 28.8 bits (63), Expect = 0.26
 Identities = 6/24 (25%), Positives = 10/24 (41%), Gaps = 9/24 (37%)

Query: 6  EKRNIEDHKRRLLATKFELKRKLY 29
          EK+ ++         K +   KLY
Sbjct: 18 EKQALK---------KLQASLKLY 32


>3oc5_A Toxin coregulated pilus biosynthesis protein F; multidomain
           protein, immunoglobulin-like (IG-like) fold, CEL
           adhesion; 2.40A {Vibrio cholerae}
          Length = 318

 Score = 27.9 bits (61), Expect = 0.48
 Identities = 21/75 (28%), Positives = 32/75 (42%), Gaps = 8/75 (10%)

Query: 2   STVSEKRNIEDHKRRLLATKFELKRKLYKSLY-----RDVNLPTEVREKYLCKLARLPRN 56
           S  ++ R  ED   RLLA  ++  +KLY   Y      D  +PT  R++ +  L      
Sbjct: 68  SDGAKTRTKEDFSARLLAGDYDSLQKLYIDFYLAQTTFDWEIPT--RDQ-IETLVNYANE 124

Query: 57  SSFTRLRNRCIFTGR 71
              +   N+   TGR
Sbjct: 125 GKLSTALNQEYITGR 139


>3k7a_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
           DNA-binding, DNA- directed RNA polymerase, isopeptide
           bond, magnesium; 3.80A {Saccharomyces cerevisiae}
          Length = 345

 Score = 26.1 bits (56), Expect = 2.5
 Identities = 9/31 (29%), Positives = 14/31 (45%), Gaps = 2/31 (6%)

Query: 26  RKLYKSLY--RDVNLPTEVREKYLCKLARLP 54
           +  YK LY  RD  +  ++    +  L  LP
Sbjct: 310 KSGYKILYEHRDKLVDPQLIANGVVSLDNLP 340


>3r0s_A Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosam acyltransferase;
           structural genomics; 2.30A {Campylobacter jejuni subsp}
          Length = 266

 Score = 24.5 bits (54), Expect = 7.4
 Identities = 7/37 (18%), Positives = 17/37 (45%)

Query: 9   NIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREK 45
           N+   +RR    + +   + +K+L+R  +L    +  
Sbjct: 198 NLVGIRRRFDKDEVDRLSRAFKTLFRQGDLKENAKNL 234


>2q14_A Phosphohydrolase; BT4208, HD domain, structural genomics, JO center
           for structural genomics, JCSG; HET: MSE ADP; 2.20A
           {Bacteroides thetaiotaomicron vpi-5482}
          Length = 410

 Score = 24.6 bits (53), Expect = 8.5
 Identities = 5/52 (9%), Positives = 19/52 (36%), Gaps = 1/52 (1%)

Query: 1   MSTVSEKRNIEDHKRRLLATKFELKRKLYKSLYRDVNLPTEVREKYLCKLAR 52
            + +    N  D     L+    + R ++K       +  +  ++   ++++
Sbjct: 290 WTALKVWSNHPDKVLSTLSLGM-INRNIFKVENSAEPIGEDRIKELTLQISQ 340


>2xot_A Amphoterin-induced protein 1; cell adhesion, neuronal protein,
          neurite growth regulation; HET: NAG BMA; 2.00A {Mus
          musculus}
          Length = 361

 Score = 24.4 bits (53), Expect = 9.9
 Identities = 10/30 (33%), Positives = 14/30 (46%), Gaps = 2/30 (6%)

Query: 37 NLPTEVREKYL--CKLARLPRNSSFTRLRN 64
          +LP+      L    L+RL    + TRL N
Sbjct: 36 SLPSYTALLDLSHNNLSRLRAEWTPTRLTN 65


  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
   0.325    0.135    0.388 

Gapped
Lambda     K      H
   0.267   0.0780    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,472,806
Number of extensions: 74473
Number of successful extensions: 167
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 20
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: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.3 bits)