RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10606
         (128 letters)



>1tyj_A Cellulosomal scaffoldin; beta sandwich, dockerin-binding module,
          alpha helix, flaps, structural protein; 1.60A
          {Bacteroides cellulosolvens} SCOP: b.2.2.2 PDB: 2y3n_A
          Length = 170

 Score = 26.7 bits (58), Expect = 1.7
 Identities = 10/39 (25%), Positives = 15/39 (38%)

Query: 6  YQCNSAYDPRCGDPFDPYSLGTVNCSLLPIPENLLHKEY 44
          YQ N  Y+     P+D  +      S +P    LL   +
Sbjct: 33 YQFNIKYNTTYLQPWDTIADEAYTDSTMPDYGTLLQGRF 71


>1e8j_A Rubredoxin; iron-sulfur-protein, zinc-substitution,
          thermostability; NMR {Desulfovibrio gigas} SCOP:
          g.41.5.1 PDB: 1rdg_A 2dsx_A 1spw_A
          Length = 52

 Score = 24.8 bits (55), Expect = 2.8
 Identities = 11/24 (45%), Positives = 11/24 (45%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
          VC  C   YDP  GDP      GT
Sbjct: 5  VCTVCGYEYDPAKGDPDSGIKPGT 28


>4rxn_A Rubredoxin; electron transfer(iron-sulfur protein); 1.20A
          {Clostridium pasteurianum} SCOP: g.41.5.1 PDB: 5rxn_A
          1bfy_A 1fhh_A 1fhm_A 1irn_A 1iro_A 1r0f_A 1r0g_A 1r0h_A
          1r0i_A 1r0j_A 1t9q_A 1c09_A 1b2j_A 1b13_A 1smm_A 1smu_A
          1smw_A 1be7_A 1t9o_A ...
          Length = 54

 Score = 24.8 bits (55), Expect = 2.9
 Identities = 11/24 (45%), Positives = 12/24 (50%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
           C  C   YDP  GDP D  + GT
Sbjct: 5  TCTVCGYIYDPEDGDPDDGVNPGT 28


>3ghp_A Cellulosomal scaffoldin adaptor protein B; linker segments, beta
          barrel, alpha helix, beta flaps, structural protein;
          2.49A {Acetivibrio cellulolyticus}
          Length = 227

 Score = 26.4 bits (57), Expect = 3.0
 Identities = 14/43 (32%), Positives = 17/43 (39%)

Query: 6  YQCNSAYDPRCGDPFDPYSLGTVNCSLLPIPENLLHKEYQTPV 48
          YQ N  YDP      +P +      S LP    LL  E   P+
Sbjct: 42 YQVNIKYDPTVLQAVNPKTGVAYTNSSLPTSGELLVSEDYGPI 84


>1yk4_A Rubredoxin, RD; electron transport; 0.69A {Pyrococcus abyssi}
          PDB: 2pya_A 1yk5_A 1bq8_A 1bq9_A* 3kyu_A 3kyv_A 3kyw_A
          3kyx_A 3kyy_A 3ryg_A 3rz6_A 3rzt_A 3ss2_A 1brf_A 1caa_A
          1cad_A 1vcx_A 1zrp_A 1iu5_A 1iu6_A ...
          Length = 52

 Score = 24.8 bits (55), Expect = 3.1
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
           C  C   YD   GDP +  S GT
Sbjct: 4  SCKICGYIYDEDEGDPDNGISPGT 27


>3kcp_B Cellulosome anchoring protein, cohesin region; dockerin, X-module,
           carbohydrate metabolism, cell WALL
           biogenesis/degradation; 1.94A {Clostridium thermocellum
           atcc 27405} PDB: 3p0d_B 2b59_A
          Length = 187

 Score = 26.3 bits (57), Expect = 3.4
 Identities = 13/52 (25%), Positives = 18/52 (34%), Gaps = 1/52 (1%)

Query: 6   YQCNSAYDPRCGDPFDPYSLGTVNCSLLPIPENLLHK-EYQTPVICRKIIQK 56
           +Q N  YDP+     DP +      S  P    +L    Y    I     +K
Sbjct: 51  FQVNIVYDPKVLMAVDPETGKEFTSSTFPPGRTVLKNNAYGPIQIADNDPEK 102


>1dx8_A Rubredoxin; electron transport, zinc-substitution; NMR
          {Guillardia theta} SCOP: g.41.5.1 PDB: 1h7v_A
          Length = 70

 Score = 24.9 bits (55), Expect = 3.9
 Identities = 9/24 (37%), Positives = 10/24 (41%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
           C  C   Y+P  GD F     GT
Sbjct: 9  ECEACGYIYEPEKGDKFAGIPPGT 32


>2v3b_B Rubredoxin 2, rubredoxin; alkane degradation, iron-sulfur
          protein, oxidoreductase, ELE transfer, electron
          transport, FAD, NAD, iron; HET: FAD; 2.45A {Pseudomonas
          aeruginosa}
          Length = 55

 Score = 24.4 bits (54), Expect = 3.9
 Identities = 8/24 (33%), Positives = 9/24 (37%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
           C  C   YD   G P +    GT
Sbjct: 5  QCVVCGFIYDEALGLPEEGIPAGT 28


>2kn9_A Rubredoxin; metalloprotein, ssgcid, structural genomics, seattle
          structural genomics center for infectious electron
          transport, iron; NMR {Mycobacterium tuberculosis}
          Length = 81

 Score = 25.1 bits (55), Expect = 4.1
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
           C QC   YD   G P D  + GT
Sbjct: 29 RCIQCGFEYDEALGWPEDGIAAGT 52


>1s24_A Rubredoxin 2; electron transport; NMR {Pseudomonas oleovorans}
          SCOP: g.41.5.1
          Length = 87

 Score = 25.1 bits (55), Expect = 4.1
 Identities = 8/24 (33%), Positives = 12/24 (50%)

Query: 4  VCYQCNSAYDPRCGDPFDPYSLGT 27
          +C  C   YD   GD  + ++ GT
Sbjct: 37 ICITCGHIYDEALGDEAEGFTPGT 60


>3l0q_A Xylulose kinase; xlylulose kinase, SGX, PSI, structural genomics,
           protein structure initiative; HET: MSE XUL EPE; 1.61A
           {Yersinia pseudotuberculosis} PDB: 3gg4_A*
          Length = 554

 Score = 25.4 bits (56), Expect = 7.9
 Identities = 3/17 (17%), Positives = 4/17 (23%)

Query: 67  CGYINEERDDCYRRTGT 83
              IN  +       G 
Sbjct: 120 AERINATKHPVLEFVGG 136


  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
   0.323    0.140    0.441 

Gapped
Lambda     K      H
   0.267   0.0776    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,975,236
Number of extensions: 107097
Number of successful extensions: 246
Number of sequences better than 10.0: 1
Number of HSP's gapped: 246
Number of HSP's successfully gapped: 32
Length of query: 128
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 45
Effective length of database: 4,384,350
Effective search space: 197295750
Effective search space used: 197295750
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 51 (23.3 bits)