RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12448
         (168 letters)



>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA
           replication, DNA-BI DNA-directed DNA polymerase,
           exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A
           {Saccharomyces cerevisiae}
          Length = 919

 Score = 73.0 bits (179), Expect = 7e-16
 Identities = 25/47 (53%), Positives = 35/47 (74%)

Query: 1   MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESILL 47
            +AEDP++VLENN+ +DS YYL NQL  P+I I +PI+GDK  + + 
Sbjct: 871 NRAEDPLFVLENNIQVDSRYYLTNQLQNPIISIVAPIIGDKQANGMF 917


>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B
           polymer alpha family polymerase, transferase; 2.10A
           {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A
           2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A*
           4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
          Length = 775

 Score = 65.2 bits (159), Expect = 4e-13
 Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 11/73 (15%)

Query: 2   KAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESILLRGDHTRTKIVSTSR 61
           +A             D+ YY+ENQ+   + RI     G + E   LR   T+        
Sbjct: 713 RAIPADEFDPTKHRYDAEYYIENQVLPAVERILKAF-GYRKED--LRYQKTKQV------ 763

Query: 62  VGALSMFVQKKQT 74
              L  +++ K  
Sbjct: 764 --GLGAWLKVKGK 774


>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A
            {Human herpesvirus 1} PDB: 1dml_B*
          Length = 1193

 Score = 52.9 bits (126), Expect = 7e-09
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 4/51 (7%)

Query: 1    MKAEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGD---KAESILLR 48
              AEDP Y + + V ++++YY  + L       F  + G+     ES+L R
Sbjct: 1099 ELAEDPAYAIAHGVALNTDYYFSHLLGAAC-VTFKALFGNNAKITESLLKR 1148


>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA
           repair, DNA-binding; HET: DNA DOC DCP; 1.92A
           {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A*
           3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
          Length = 786

 Score = 45.9 bits (109), Expect = 2e-06
 Identities = 10/44 (22%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 3   AEDPIYVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESIL 46
              P  +     P+D  +YL  QL      I  P + D   +++
Sbjct: 737 TNGPEPLDYQRSPLDYEHYLTRQLQPVAEGIL-PFIEDNFATLM 779


>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET:
           DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5
           e.8.1.1
          Length = 847

 Score = 41.4 bits (97), Expect = 6e-05
 Identities = 10/38 (26%), Positives = 13/38 (34%), Gaps = 2/38 (5%)

Query: 8   YVLENNVPIDSNYYLENQLSKPLIRIFSPILGDKAESI 45
             L     ID+  YLE  L     +I     G   + I
Sbjct: 794 VQLAKVTEIDAEKYLE-ALRSTFEQILRAF-GVSWDEI 829


>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 = 33.7 bits (76), Expect = 0.027
 Identities = 21/164 (12%), Positives = 46/164 (28%), Gaps = 38/164 (23%)

Query: 2   KAEDPIYVLEN-NVPIDSNYYLENQLSKPLIRIFSPI--LGDKAESILLRGDHTRTKI-- 56
             E  + +L+     ID N+      S     I   I  +  +   +L    +    +  
Sbjct: 194 SPETVLEMLQKLLYQIDPNW---TSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVL 250

Query: 57  --VSTSRVGALSMFVQKKQTCIGCKVVL--HDTSLSNALCNFCLAKEKQYYEAENDKYQQ 112
             V  ++    + F       + CK++L      +++ L           + + +     
Sbjct: 251 LNVQNAKA--WNAFN------LSCKILLTTRFKQVTDFLSA-----ATTTHISLDHHSMT 297

Query: 113 LEKK----FCQLWTQC-------QTCQGS-LHEQVICTS-RDCP 143
           L           +  C       +    +     +I  S RD  
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGL 341


>3ghg_C Fibrinogen gamma chain; triple-stranded coiled coil, beta sheets,
           alpha helices, AMY amyloidosis, blood coagulation,
           disease mutation, glycoprot phosphoprotein; HET: NAG NDG
           BMA MAN GAL SIA; 2.90A {Homo sapiens} PDB: 1deq_C
          Length = 411

 Score = 27.9 bits (62), Expect = 1.9
 Identities = 15/51 (29%), Positives = 21/51 (41%)

Query: 103 YEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQS 153
           Y + N K   L++K  QL  QCQ       +    T +DC     +   QS
Sbjct: 114 YNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQDIANKGAKQS 164


>1d3y_A DNA topoisomerase VI A subunit; DNA binding protein, SPO11 homolog;
           HET: DNA; 2.00A {Methanocaldococcus jannaschii} SCOP:
           e.12.1.1
          Length = 301

 Score = 27.5 bits (60), Expect = 2.3
 Identities = 8/35 (22%), Positives = 13/35 (37%), Gaps = 2/35 (5%)

Query: 115 KKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRK 149
           K F Q     +  +  L      T R+   +Y+ K
Sbjct: 6   KIFAQTTKMLEFAKQLLETDDFSTLRE--AYYVSK 38


>3aup_A SBG7S, BG, basic 7S globulin; pepsin-like fold, plant protein;
           1.91A {Glycine max}
          Length = 403

 Score = 27.0 bits (59), Expect = 3.5
 Identities = 10/47 (21%), Positives = 14/47 (29%), Gaps = 5/47 (10%)

Query: 120 LWTQCQTCQGSL-HEQVICTSRDCPIFYMRKKVQSCGHNVKRARGVC 165
           LW  C+    S  ++   C S  C           C      +R  C
Sbjct: 47  LWVNCEQQYSSKTYQAPFCHSTQCSRA----NTHQCLSCPAASRPGC 89


>1fzc_C Fibrin; blood coagulation, plasma protein, crosslinking; HET: NAG
           MAN; 2.30A {Homo sapiens} SCOP: d.171.1.1 h.1.8.1 PDB:
           1fzb_C* 1fza_C* 1fze_C* 1fzf_C* 1fzg_C* 2xnx_C 2xny_C
           3e1i_C* 2hlo_C* 1n8e_C 1n86_C* 2q9i_C* 2z4e_C* 2h43_C*
           2hod_C* 2hpc_C* 3h32_C* 1re3_C* 1ltj_C* 1lt9_C* ...
          Length = 319

 Score = 26.3 bits (58), Expect = 4.7
 Identities = 15/51 (29%), Positives = 21/51 (41%)

Query: 103 YEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQS 153
           Y + N K   L++K  QL  QCQ       +    T +DC     +   QS
Sbjct: 27  YNSNNQKIVNLKEKVAQLEAQCQEPCKDTVQIHDITGKDCQDIANKGAKQS 77


>1m1j_C Fibrinogen gamma chain; coiled coils, disulfide rings, fibrinogen,
           blood clotting; HET: NDG NAG; 2.70A {Gallus gallus}
           SCOP: d.171.1.1 h.1.8.1 PDB: 1ei3_C
          Length = 409

 Score = 26.4 bits (58), Expect = 4.8
 Identities = 14/51 (27%), Positives = 22/51 (43%)

Query: 103 YEAENDKYQQLEKKFCQLWTQCQTCQGSLHEQVICTSRDCPIFYMRKKVQS 153
           +   ++K  QL++K  QL + CQ       E    T RDC     +   +S
Sbjct: 114 HIMNSNKITQLKQKIAQLESHCQEPCKDTAEIQETTGRDCQDIANKGARKS 164


>2yfg_A NADP-specific glutamate dehydrogenase; oxidoreductase; 2.50A
           {Escherichia coli} PDB: 3sbo_A 2yfg_E
          Length = 447

 Score = 26.1 bits (58), Expect = 7.6
 Identities = 8/34 (23%), Positives = 14/34 (41%)

Query: 48  RGDHTRTKIVSTSRVGALSMFVQKKQTCIGCKVV 81
            G       VS S  G ++ +  +K    G +V+
Sbjct: 226 HGMGFEGMRVSVSGSGNVAQYAIEKAMEFGARVI 259


  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
   0.322    0.134    0.411 

Gapped
Lambda     K      H
   0.267   0.0531    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,348,226
Number of extensions: 120118
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 32
Length of query: 168
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 81
Effective length of database: 4,272,666
Effective search space: 346085946
Effective search space used: 346085946
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 (21.9 bits)
S2: 54 (25.0 bits)