RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11170
         (111 letters)



>2ck3_I ATP synthase subunit epsilon\, mitochondrial; hydrolase; HET: ANP
          ADP; 1.9A {Bos taurus} PDB: 1e79_I* 1h8e_I* 2jdi_I*
          2v7q_I* 2wss_I* 2w6j_I 2w6h_I 2w6i_I 2xnd_I*
          Length = 50

 Score = 63.5 bits (154), Expect = 3e-15
 Identities = 20/39 (51%), Positives = 26/39 (66%)

Query: 39 YIQYSNIAARTLRRALKTEFRADAEKREESFIRITPWKD 77
          YI+YS I A+ +R ALKTEF+A+A K   S I+I   K 
Sbjct: 11 YIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVKVKK 49


>3oee_I ATP synthase subunit epsilon; ATP phosphatase, F1F0 ATPase, ATP
          synthesis, H ADP, PO4, mitochondria; HET: ANP; 2.74A
          {Saccharomyces cerevisiae} PDB: 2wpd_I* 3fks_I 3oe7_I*
          2hld_I* 3oeh_I* 3ofn_I* 2xok_I* 3zry_I*
          Length = 61

 Score = 62.7 bits (152), Expect = 6e-15
 Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 4/50 (8%)

Query: 39 YIQYSNIAARTLRRALKTEFRADA-EKREESFIRITPWKDGKPIRHYSEP 87
          Y  Y N+AA+ +R +LKTE +  +   R ++    T +K+G      SEP
Sbjct: 10 YAAYLNVAAQAIRSSLKTELQTASVLNRSQTDAFYTQYKNGTAA---SEP 56


>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 = 28.7 bits (63), Expect = 0.42
 Identities = 14/108 (12%), Positives = 30/108 (27%), Gaps = 24/108 (22%)

Query: 18  NMGYDDKRQAIQFSAEVLN-----RCYIQYS------NIAARTLRRALKTEFRADAEKRE 66
           ++  D     I+ S  VL      + + + S      +I    L        ++D     
Sbjct: 349 HVNCDKLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVV 408

Query: 67  ESFIR---ITPWKDGKPIRHYSEPLHYVTPILLQDDLDIFSISTPLLH 111
               +   +   K  K        +       +  +L +   +   LH
Sbjct: 409 NKLHKYSLVE--KQPKESTIS---IP-----SIYLELKVKLENEYALH 446


>1vk5_A Expressed protein; structural genomics, unknown function, protein
          structur initiative, center for eukaryotic structural
          genomics, CESG; HET: CPS; 1.60A {Arabidopsis thaliana}
          SCOP: a.220.1.1 PDB: 2q3t_A* 3gan_A*
          Length = 157

 Score = 26.7 bits (58), Expect = 1.3
 Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 2/35 (5%)

Query: 65 REESFIRITPWKD-GKPIRH-YSEPLHYVTPILLQ 97
             S I  T W      ++  Y +PLHY+T +LLQ
Sbjct: 57 NRGSLIPFTSWVGLSISMKQLYGQPLHYLTNVLLQ 91


>2gpi_A Conserved hypothetical protein; transcriptional regulation of the
          shikimate pathway, structu genomics, joint center for
          structural genomics; HET: MSE; 1.60A {Shewanella
          loihica} SCOP: d.354.1.1
          Length = 91

 Score = 26.1 bits (57), Expect = 1.6
 Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 11/62 (17%)

Query: 21 YDDKRQAIQFSAEV---LNRCYIQYSNIAARTLRR--------ALKTEFRADAEKREESF 69
          +D +  AI F+A+    +  CYI    +      +        +L  +FR D E++ E  
Sbjct: 14 WDVQLSAIHFTAQQQGMVIDCYIGQKVLEHLAAEKINNSEQALSLFEQFRFDIEEQAEKL 73

Query: 70 IR 71
          I 
Sbjct: 74 IE 75


>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 = 1.7
 Identities = 26/135 (19%), Positives = 46/135 (34%), Gaps = 51/135 (37%)

Query: 2   FVTKIPSRYPLLTLMSNMGYDDKRQAIQFSAEVLNRCYIQYSNIAART-------LRRAL 54
           ++  IP   PL+ +            IQ +       Y+    + A+        LR  L
Sbjct: 230 YLLSIPISCPLIGV------------IQLA------HYV----VTAKLLGFTPGELRSYL 267

Query: 55  K--TEFRAD--------AEKREESF-------IRITPWKDGKPIR-HYSEPLHYVTPILL 96
           K  T                  ESF       I +  +  G  +R + + P   + P +L
Sbjct: 268 KGATGHSQGLVTAVAIAETDSWESFFVSVRKAITVLFFI-G--VRCYEAYPNTSLPPSIL 324

Query: 97  QDDLDI-FSISTPLL 110
           +D L+    + +P+L
Sbjct: 325 EDSLENNEGVPSPML 339


>2l82_A Designed protein OR32; structural genomics, northeast structural
           genomics consortiu PSI-biology, protein structure
           initiative, de novo protein; NMR {Artificial gene}
          Length = 162

 Score = 25.9 bits (56), Expect = 2.6
 Identities = 18/63 (28%), Positives = 29/63 (46%), Gaps = 4/63 (6%)

Query: 3   VTKIPSRYPLLTLMSNMGYDDKRQAIQFSAEVLNR---CYIQYSNIAARTLRRALKTEFR 59
           + +I  RYP L ++  +  DDK     F  E   R    ++ Y+N      R+  + EFR
Sbjct: 68  IREIWERYPQLDVVVIVTTDDKEWIKDFIEEAKERGVEVFVVYNN-KDDDRRKEAQQEFR 126

Query: 60  ADA 62
           +D 
Sbjct: 127 SDG 129


>3ln3_A Dihydrodiol dehydrogenase; putative reductase, structural genomics,
           joint center for structural genomics, JCSG, protein
           structure initiative, PSI-2; HET: MLY MSE NAD; 1.18A
           {Mus musculus}
          Length = 324

 Score = 25.3 bits (55), Expect = 4.9
 Identities = 11/58 (18%), Positives = 22/58 (37%)

Query: 52  RALKTEFRADAEKREESFIRITPWKDGKPIRHYSEPLHYVTPILLQDDLDIFSISTPL 109
           +A+++   A    RE+ F+    W            L      L  D +D++ +  P+
Sbjct: 64  QAIQSXIXAGVVXREDLFVTTKLWCTCFRPELVXPALEXSLXXLQLDYVDLYIMHYPV 121


>1ss6_A P47, NSFL1 cofactor P47, P47 protein, P97; , SEP, signaling
          protein; NMR {Homo sapiens} SCOP: d.245.1.1
          Length = 102

 Score = 24.4 bits (53), Expect = 5.8
 Identities = 6/34 (17%), Positives = 12/34 (35%), Gaps = 5/34 (14%)

Query: 59 RADAEKREESFIRITPWKDG-----KPIRHYSEP 87
                 ++  + +  WK G       +R Y +P
Sbjct: 3  EKRQHSSQDVHVVLKLWKSGFSLDNGELRSYQDP 36


>2gru_A 2-deoxy-scyllo-inosose synthase; aminoglycoside,
           2-deoxystreptamine, dehydroquinate synthase, lyase; HET:
           NAD EXO CAK; 2.15A {Bacillus circulans} PDB: 2d2x_A*
          Length = 368

 Score = 24.6 bits (54), Expect = 8.1
 Identities = 11/62 (17%), Positives = 24/62 (38%), Gaps = 9/62 (14%)

Query: 4   TKIPSRYPLLTLMSNMGYDDKRQAIQFSAEVLN--------RCYIQYSNIAARTLRRALK 55
             IP +    ++   + +D+KR  I+   + L         +  + Y+      +R+ L 
Sbjct: 302 QDIPLKSDPDSIFHYLIHDNKRGYIKLDEDNLGMILLSGVGKPAM-YNQTLLTPVRKTLI 360

Query: 56  TE 57
            E
Sbjct: 361 KE 362


>1v33_A DNA primase small subunit; nucleotidyl transferase, riken
          structural genomics/proteomics initiative, RSGI,
          structural genomics; HET: DNA; 1.80A {Pyrococcus
          horikoshii} SCOP: d.264.1.1 PDB: 1v34_A* 1g71_A*
          Length = 366

 Score = 24.5 bits (52), Expect = 9.7
 Identities = 6/25 (24%), Positives = 7/25 (28%), Gaps = 3/25 (12%)

Query: 61 DAEKREESFIRITPWKDGKPIRHYS 85
            E RE  F       +G   R   
Sbjct: 51 TLELREFGF---DHSGEGPSDRKNQ 72


  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
   0.324    0.138    0.410 

Gapped
Lambda     K      H
   0.267   0.0555    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,701,333
Number of extensions: 89653
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 250
Number of HSP's successfully gapped: 14
Length of query: 111
Length of database: 6,701,793
Length adjustment: 75
Effective length of query: 36
Effective length of database: 4,607,718
Effective search space: 165877848
Effective search space used: 165877848
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 (21.5 bits)
S2: 51 (23.8 bits)