RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9435
         (106 letters)



>2wdq_C Succinate dehydrogenase cytochrome B556 subunit; succinate
          dehydrogenase activity, cell inner membrane, trica acid
          cycle; HET: FAD HEM CBE; 2.40A {Escherichia coli} PDB:
          1nen_C* 2acz_C* 1nek_C* 2wdr_C* 2wdv_C* 2wp9_C* 2ws3_C*
          2wu5_C* 2wu2_C*
          Length = 129

 Score = 65.9 bits (161), Expect = 2e-15
 Identities = 14/43 (32%), Positives = 21/43 (48%)

Query: 48 RNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLA 90
          RN +  RP++  L   +  IT++ SI HR +GV        L 
Sbjct: 3  RNVKKQRPVNLDLQTIRFPITAIASILHRVSGVITFVAVGILL 45


>2h88_C Succinate dehydrogenase cytochrome B, large subun; complex II,
          membrane protein, heme protein, iron sulfur PROT
          cytochrome B, oxidoreductase; HET: FAD BHG HEM UNL;
          1.74A {Gallus gallus} PDB: 2h89_C* 1yq3_C* 1yq4_C*
          2fbw_C* 2wqy_C*
          Length = 140

 Score = 63.9 bits (155), Expect = 1e-14
 Identities = 23/56 (41%), Positives = 31/56 (55%)

Query: 35 APTGVPSKEGHAVRNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLA 90
          A T          +N +  RPLSPH++IYK  +   +SITHRGTGVAL+      +
Sbjct: 2  ATTAKEEMARFWEKNTKSSRPLSPHISIYKWSLPMAMSITHRGTGVALSLGVSLFS 57


>1zoy_C Large cytochrome binding protein, FAD-binding protein; succinate,
          ubiquinone oxidoreductase, mitochondrial respiratory
          complex II; HET: FAD HEM EPH UQ1; 2.40A {Sus scrofa}
          PDB: 1zp0_C* 3abv_C* 3ae1_C* 3ae2_C* 3ae3_C* 3ae4_C*
          3ae5_C* 3ae6_C* 3ae7_C* 3ae8_C* 3ae9_C* 3aea_C* 3aeb_C*
          3aec_C* 3aed_C* 3aee_C* 3aef_C* 3aeg_C* 3sfd_C* 3sfe_C*
          Length = 140

 Score = 62.7 bits (152), Expect = 4e-14
 Identities = 20/43 (46%), Positives = 27/43 (62%)

Query: 48 RNERLGRPLSPHLTIYKLQITSVLSITHRGTGVALTAYALGLA 90
          +N    RPLSPH+TIY+  +   +SI HRGTG+AL+A      
Sbjct: 15 KNLGSNRPLSPHITIYRWSLPMAMSICHRGTGIALSAGVSLFG 57


>3vr8_C Cytochrome B-large subunit; membrane protein, reductase,
          mitochondria MEMB oxidoreductase; HET: FAD HEM RQX EPH;
          2.81A {Ascaris suum} PDB: 3vrb_C*
          Length = 188

 Score = 59.1 bits (142), Expect = 2e-12
 Identities = 27/91 (29%), Positives = 47/91 (51%), Gaps = 2/91 (2%)

Query: 1  MNSIFKLSTLCNPIASSHLRLLPHIRTITIKPVAAPTGVPSK-EGHAVRNERLGRPLSPH 59
          M+ +   +TLC  +  + ++ +  ++T   +  A  T +      + +R   L RP++PH
Sbjct: 1  MSLLPYNATLCRVLRHN-VKFIRSVQTSAARVSAEKTPIQVWGWDYLMRQRALKRPIAPH 59

Query: 60 LTIYKLQITSVLSITHRGTGVALTAYALGLA 90
          LTIYK Q+T ++S  HR TG A+    L   
Sbjct: 60 LTIYKPQMTWMVSGLHRVTGCAMAGTLLIGG 90


>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 = 28.9 bits (64), Expect = 0.34
 Identities = 26/109 (23%), Positives = 36/109 (33%), Gaps = 34/109 (31%)

Query: 5   FKLSTLCNPIAS----SHLR-----LLP-HIRTITIKPVAAPTGVPSKEGHAVRNERLGR 54
           F    +  P+      S LR     +    +  I   PV   T    K  H +     G 
Sbjct: 450 FNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHIL---DFG- 505

Query: 55  PLSPHLTIYKLQITSVLSITHR---GTGVALTAYALGLAGVGLTTDINS 100
           P            + +  +THR   GTGV +      +AG   T DIN 
Sbjct: 506 PGG---------ASGLGVLTHRNKDGTGVRVI-----VAG---TLDINP 537


>2yy8_A ATRM56, UPF0106 protein PH0461; DEEP trefoil knot, structural
           genomics, NPPSFA; HET: SAM MTA; 2.48A {Pyrococcus
           horikoshii}
          Length = 201

 Score = 27.2 bits (60), Expect = 0.80
 Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 7/41 (17%)

Query: 69  SVLSITHRG-------TGVALTAYALGLAGVGLTTDINSVV 102
            VL + HR        T VALTA A G  G+ + ++ +  V
Sbjct: 3   VVLRLGHRPERDKRVTTHVALTARAFGADGIIIASEEDEKV 43


>2o3a_A UPF0106 protein AF_0751; structural genomics, unknown function,
           PSI-2, protein structure initiative; 2.20A
           {Archaeoglobus fulgidus} SCOP: c.116.1.8
          Length = 178

 Score = 25.5 bits (56), Expect = 3.2
 Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 7/43 (16%)

Query: 69  SVLSITHRG-------TGVALTAYALGLAGVGLTTDINSVVPT 104
            VL + HR        T VALTA A G  G+   T+  SV  +
Sbjct: 6   YVLRLGHRPERDKRISTHVALTARAFGAKGIYFDTEDKSVFES 48


  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
   0.320    0.135    0.392 

Gapped
Lambda     K      H
   0.267   0.0473    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,512,490
Number of extensions: 81177
Number of successful extensions: 181
Number of sequences better than 10.0: 1
Number of HSP's gapped: 181
Number of HSP's successfully gapped: 9
Length of query: 106
Length of database: 6,701,793
Length adjustment: 71
Effective length of query: 35
Effective length of database: 4,719,402
Effective search space: 165179070
Effective search space used: 165179070
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: 51 (24.0 bits)