RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8226
         (115 letters)



>3h7h_A Transcription elongation factor SPT4; helices surrounding beta
           sheet, activator, ME binding, nucleus, repressor,
           transcription regulation; 1.55A {Homo sapiens}
          Length = 120

 Score = 99.3 bits (247), Expect = 2e-28
 Identities = 37/56 (66%), Positives = 48/56 (85%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRIRR 113
           T DQFE+DGCDNCD +L MK +R+ VY+CTSS+FDG+IA+M P+DSWV+KWQR+  
Sbjct: 27  TIDQFEYDGCDNCDAYLQMKGNREMVYDCTSSSFDGIIAMMSPEDSWVSKWQRVSN 82


>2exu_A Transcription initiation protein SPT4/SPT5; helixs surrounding beta
           sheet; 2.23A {Saccharomyces cerevisiae}
          Length = 200

 Score = 87.4 bits (216), Expect = 5e-23
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 58  TFDQFEFDGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           T ++F  DGC NC           +   CTS +F+G++ +  P  SWVAKW  +
Sbjct: 15  TTNEFNRDGCPNCQGIFEEA--GVSTMECTSPSFEGLVGMCKPTKSWVAKWLSV 66


>1ryq_A DNA-directed RNA polymerase, subunit E''; structural genomics,
           zinc, PSI, protein structure initiative; 1.38A
           {Pyrococcus furiosus} SCOP: g.41.9.3 PDB: 3qqc_E
          Length = 69

 Score = 37.4 bits (87), Expect = 6e-05
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 8/51 (15%)

Query: 67  CDNCDEFLHMKNSRDNVYNC----TSSNFDGMIALMDPKDSWVAKWQRIRR 113
           C +C    H   S D    C     S  +  ++ ++D ++S +AK    + 
Sbjct: 14  CRHC----HYITSEDRCPVCGSRDLSEEWFDLVIIVDVENSEIAKKIGAKV 60


>3p8b_A DNA-directed RNA polymerase, subunit E''; transcription elongation
           factor, RNA polymerase, transferase transcription
           complex; 1.80A {Pyrococcus furiosus}
          Length = 81

 Score = 37.1 bits (86), Expect = 9e-05
 Identities = 8/47 (17%), Positives = 16/47 (34%), Gaps = 12/47 (25%)

Query: 65  DGCDNCDEFLHMKNSRDNVYNCTSSNFDGMIALMDPKDSWVAKWQRI 111
           D C  C                 S  +  ++ ++D ++S +AK    
Sbjct: 36  DRCPVCGS------------RDLSEEWFDLVIIVDVENSEIAKKIGA 70


>3lpe_B DNA-directed RNA polymerase subunit E''; transcription regulation,
           SPT4, SPT5, NUSG, archaea, evoluti directed RNA
           polymerase; 1.90A {Methanocaldococcus jannaschii}
          Length = 59

 Score = 32.7 bits (75), Expect = 0.003
 Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 7/44 (15%)

Query: 67  CDNCDEFLHMKNSRDNVYNC---TSSNFDGMIALMDPKDSWVAK 107
           C  C        + +    C   TS N+ G++ +++P+ S +AK
Sbjct: 4   CLKC----KYLTNDEICPICHSPTSENWIGLLIVINPEKSEIAK 43


>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
            mRNA, multiprotein complex; HET: UTP; 2.30A
            {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
            1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
            1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
            1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
          Length = 1224

 Score = 27.9 bits (62), Expect = 0.74
 Identities = 8/41 (19%), Positives = 12/41 (29%)

Query: 47   SAETINPRTTSTFDQFEFDGCDNCDEFLHMKNSRDNVYNCT 87
            +A  +  R     D F    C  C     +     N + C 
Sbjct: 1143 AASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECK 1183


>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 = 26.7 bits (58), Expect = 2.4
 Identities = 19/107 (17%), Positives = 35/107 (32%), Gaps = 27/107 (25%)

Query: 25  LKVVGVHNEDHRPWTIDPIPSASAETINPRTTSTFDQFEFDGCDNCDEFLH-----MKNS 79
           LK +    +D        +P     T NPR  S   +   DG    D + H     +   
Sbjct: 308 LKYLDCRPQD--------LPR-EVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI 358

Query: 80  RDNVYNCTSSN-----FDGMIALMDPKDSWV-AK-----WQRIRRTD 115
            ++  N          FD  +++  P  + +        W  + ++D
Sbjct: 359 IESSLNVLEPAEYRKMFD-RLSVF-PPSAHIPTILLSLIWFDVIKSD 403


>4a27_A Synaptic vesicle membrane protein VAT-1 homolog-L;
          oxidoreductase; 2.10A {Homo sapiens}
          Length = 349

 Score = 25.3 bits (56), Expect = 5.3
 Identities = 5/18 (27%), Positives = 8/18 (44%)

Query: 13 YRPPPKPSTLAGLKVVGV 30
             PPK   + G +  G+
Sbjct: 54 IDNPPKTPLVPGFECSGI 71


>3pi7_A NADH oxidoreductase; groes-like fold, NAD(P)-binding rossmann
          fold, structural GE joint center for structural
          genomics, JCSG; HET: MSE; 1.71A {Mesorhizobium loti}
          Length = 349

 Score = 25.3 bits (56), Expect = 5.5
 Identities = 6/18 (33%), Positives = 7/18 (38%)

Query: 13 YRPPPKPSTLAGLKVVGV 30
          Y  P      AG + VG 
Sbjct: 73 YGQPRVKGRPAGFEGVGT 90


>2f9y_B Acetyl-coenzyme A carboxylase carboxyl transferas beta; zinc
          ribbon, crotonase superfamily, spiral domain, ligase;
          3.20A {Escherichia coli} SCOP: c.14.1.4
          Length = 304

 Score = 24.5 bits (54), Expect = 9.9
 Identities = 6/25 (24%), Positives = 11/25 (44%)

Query: 67 CDNCDEFLHMKNSRDNVYNCTSSNF 91
          CD+C + L+      N+  C   + 
Sbjct: 27 CDSCGQVLYRAELERNLEVCPKCDH 51


  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
   0.319    0.136    0.442 

Gapped
Lambda     K      H
   0.267   0.0771    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,895,555
Number of extensions: 96091
Number of successful extensions: 277
Number of sequences better than 10.0: 1
Number of HSP's gapped: 276
Number of HSP's successfully gapped: 15
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
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 (23.3 bits)