RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy7189
         (120 letters)



>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 = 40.6 bits (94), Expect = 4e-05
 Identities = 22/140 (15%), Positives = 39/140 (27%), Gaps = 33/140 (23%)

Query: 10  IYW--VGEGKKYRDFAEYLREL---------TRAQFVSNNKFTIEEEETLKKNLASLKRL 58
           I+W  +          E L++L         +R+   SN K  I   +   + L   K  
Sbjct: 184 IFWLNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243

Query: 59  SE------DIYNKKYPRTFQ-------TS-----ASGLNGKECNTLLSQEFLDAMRED-S 99
                   ++ N K    F        T+        L+      +        +  D  
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 100 KGMFSKLFKRKDKYKKDLKS 119
           K +  K    +    +DL  
Sbjct: 304 KSLLLKYLDCR---PQDLPR 320


>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 = 32.6 bits (73), Expect = 0.016
 Identities = 12/35 (34%), Positives = 16/35 (45%), Gaps = 12/35 (34%)

Query: 44 EEETLKKNLASLKRLSEDIYNKKYPRTFQTSASGL 78
          E++ LKK  ASLK  ++D            SA  L
Sbjct: 18 EKQALKKLQASLKLYADD------------SAPAL 40


>2fp4_B Succinyl-COA ligase [GDP-forming] beta-chain, mitochondrial; active
           site phosphohistidine residue; HET: NEP GTP; 2.08A {Sus
           scrofa} SCOP: c.23.4.1 d.142.1.4 PDB: 2fpg_B* 2fpi_B*
           2fpp_B* 1euc_B* 1eud_B*
          Length = 395

 Score = 26.3 bits (59), Expect = 2.9
 Identities = 13/50 (26%), Positives = 22/50 (44%), Gaps = 4/50 (8%)

Query: 48  LKKNLASLKRLSEDIYNKKYPRTFQTSASGLNGKECNTLLSQEFLDAMRE 97
           L K+   + +L++ +       T QT      G + N ++  E LD  RE
Sbjct: 69  LTKDPEVVGQLAKQMIGYNL-ATKQTPK---EGVKVNKVMVAEALDISRE 114


>2qfy_A Isocitrate dehydrogenase [NADP]; rossmann fold, oxidoreductase;
           HET: AKG; 2.10A {Saccharomyces cerevisiae} PDB: 2qfw_A*
           2qfx_A* 2qfv_A*
          Length = 427

 Score = 26.3 bits (57), Expect = 3.4
 Identities = 11/53 (20%), Positives = 23/53 (43%)

Query: 4   LYQVVVIYWVGEGKKYRDFAEYLRELTRAQFVSNNKFTIEEEETLKKNLASLK 56
           L    +     +G   +D A       R+ +V+  +F    E+ L+K + S++
Sbjct: 375 LESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSIE 427


>2nu8_B SCS-beta, succinyl-COA synthetase beta chain; citric acid cycle,
           heterotetramer, ligase, ATP-grAsp fold, R fold; HET:
           COA; 2.15A {Escherichia coli} SCOP: c.23.4.1 d.142.1.4
           PDB: 1scu_B* 2nu6_B* 1jkj_B* 2nu7_B* 2nu9_B* 2nua_B*
           2scu_B* 1jll_B* 1cqj_B* 1cqi_B*
          Length = 388

 Score = 25.5 bits (57), Expect = 4.6
 Identities = 12/48 (25%), Positives = 23/48 (47%), Gaps = 4/48 (8%)

Query: 50  KNLASLKRLSEDIYNKKYPRTFQTSASGLNGKECNTLLSQEFLDAMRE 97
            +   ++  +E+   K+   T+QT A   NG+  N +L +   D  +E
Sbjct: 64  NSKEDIRAFAENWLGKRL-VTYQTDA---NGQPVNQILVEAATDIAKE 107


>2i88_A Colicin-E1; protein-membrane interactions, toxin-membrane
          interactions, toxin structure, voltage-gated channel,
          membrane protein; 2.50A {Escherichia coli}
          Length = 191

 Score = 25.4 bits (55), Expect = 5.1
 Identities = 13/48 (27%), Positives = 23/48 (47%)

Query: 10 IYWVGEGKKYRDFAEYLRELTRAQFVSNNKFTIEEEETLKKNLASLKR 57
          +    +GKK  +  E L    + + V N KF+  + + +   LAS+K 
Sbjct: 43 LADKSKGKKIGNVNEALAAFEKYKDVLNKKFSKADRDAIFNALASVKY 90


>1ziw_A TOLL-like receptor 3; innate immunity, immune system; HET: NDG NAG;
           2.10A {Homo sapiens} PDB: 2a0z_A* 3cig_A* 3ciy_A*
          Length = 680

 Score = 25.7 bits (57), Expect = 5.4
 Identities = 5/23 (21%), Positives = 8/23 (34%)

Query: 36  SNNKFTIEEEETLKKNLASLKRL 58
             N  T  E++       +L  L
Sbjct: 592 QKNLITSVEKKVFGPAFRNLTEL 614


>3u1u_A RNA polymerase-associated protein RTF1 homolog; plus-3,
           transcription elongation, structural genomics, struc
           genomics consortium, SGC; 1.80A {Homo sapiens} PDB:
           2db9_A
          Length = 137

 Score = 24.9 bits (54), Expect = 6.4
 Identities = 21/77 (27%), Positives = 31/77 (40%), Gaps = 14/77 (18%)

Query: 5   YQVVVIYWVGEGKKYRDFAE-----YLR-------ELTRAQFVSNNKFTIEEEETLKKNL 52
           Y+V  I  V E  K            L+        + R +FVSN +FT  E    K+ +
Sbjct: 55  YRVAEITGVVETAKVYQLGGTRTNKGLQLRHGNDQRVFRLEFVSNQEFTESEFMKWKEAM 114

Query: 53  --ASLKRLSEDIYNKKY 67
             A ++  + D  NKK 
Sbjct: 115 FSAGMQLPTLDEINKKE 131


>2i7t_A Cleavage and polyadenylation specificity factor 73 kDa subunit;
           metallo-B-lactamase, PRE-mRNA processing, artemis, V(D)J
           recombination; 2.10A {Homo sapiens} SCOP: d.157.1.10
           PDB: 2i7v_A
          Length = 459

 Score = 24.9 bits (55), Expect = 8.8
 Identities = 8/31 (25%), Positives = 13/31 (41%)

Query: 19  YRDFAEYLRELTRAQFVSNNKFTIEEEETLK 49
           Y+ +   + +  R Q   NN F  +    LK
Sbjct: 282 YQTYVNAMNDKIRKQININNPFVFKHISNLK 312


  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
   0.316    0.132    0.371 

Gapped
Lambda     K      H
   0.267   0.0785    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,770,164
Number of extensions: 91549
Number of successful extensions: 366
Number of sequences better than 10.0: 1
Number of HSP's gapped: 364
Number of HSP's successfully gapped: 27
Length of query: 120
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 38
Effective length of database: 4,412,271
Effective search space: 167666298
Effective search space used: 167666298
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (23.3 bits)