RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5744
         (157 letters)



>1vd4_A Transcription initiation factor IIE, alpha subunit; zinc finger;
           NMR {Homo sapiens} SCOP: g.41.3.1
          Length = 62

 Score = 44.9 bits (106), Expect = 2e-07
 Identities = 19/28 (67%), Positives = 24/28 (85%)

Query: 116 RMEMEERDATSRSSFKCPRCLKTFTDLE 143
           R+E +ERD+T+R+SFKCP C  TFTDLE
Sbjct: 1   RIETDERDSTNRASFKCPVCSSTFTDLE 28


>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 = 33.9 bits (77), Expect = 0.019
 Identities = 16/74 (21%), Positives = 32/74 (43%), Gaps = 10/74 (13%)

Query: 83   TGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSRSSFKCPR--CLKT-F 139
             G  GK  + NY  + ++T V+       + +   E+ E   ++  +F+  +     T F
Sbjct: 1677 GGEKGKRIRENYSAMIFETIVDGKLKTEKIFK---EINEH--STSYTFRSEKGLLSATQF 1731

Query: 140  TDLEPCLLVLWCAC 153
            T  +P L ++  A 
Sbjct: 1732 T--QPALTLMEKAA 1743


>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 = 29.4 bits (65), Expect = 0.58
 Identities = 28/154 (18%), Positives = 47/154 (30%), Gaps = 50/154 (32%)

Query: 23  LVVRGFYSIEDSLI------IDMLVRNPCMKEDDICELLKFERKMLRARISTLKND---- 72
           L+   F  + D L       I +   +  +  D++  LL    K L  R   L  +    
Sbjct: 269 LLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKSLL---LKYLDCRPQDLPREVLTT 325

Query: 73  -----KIIQTRLRMETGLDGKAQKVNYYFINYQTFVNIVKYKLDVMRKRMEMEERDATSR 127
                 II   +R     DG A   N+  +N      I++  L+V+ +  E  +      
Sbjct: 326 NPRRLSIIAESIR-----DGLATWDNWKHVNCDKLTTIIESSLNVL-EPAEYRKM----- 374

Query: 128 SSFKCPRCLKTFTDL----------EPCLLVLWC 151
                      F  L             L ++W 
Sbjct: 375 -----------FDRLSVFPPSAHIPTILLSLIWF 397



 Score = 26.4 bits (57), Expect = 5.0
 Identities = 33/172 (19%), Positives = 64/172 (37%), Gaps = 33/172 (19%)

Query: 5   DEGYVHTEVPTSLKQLSRLVVRGFYSIEDSLIIDMLVRNPCMKEDDICELLKFERKMLRA 64
           +  ++ + + T  +Q S ++ R +    D L  D    N    + ++  L  + +  LR 
Sbjct: 90  NYKFLMSPIKTEQRQPS-MMTRMYIEQRDRLYND----NQVFAKYNVSRLQPYLK--LRQ 142

Query: 65  RISTLKNDKII---------QTRLRMETGLDGKAQKVNYYFINYQTF--VNIVKYKLDVM 113
            +  L+  K +         +T + ++  L  K Q    + I +      N  +  L+++
Sbjct: 143 ALLELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEML 202

Query: 114 RKRMEMEERDATSRSSFKCP------------RCLKTFTDLEPCLLVL---W 150
           +K +   + + TSRS                 R L      E CLLVL    
Sbjct: 203 QKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254


>3k1f_M Transcription initiation factor IIB; RNA polymerase II, TFIIB,
           transcription factor, DNA-binding, DNA-directed RNA
           polymerase; 4.30A {Saccharomyces cerevisiae}
          Length = 197

 Score = 26.2 bits (57), Expect = 5.2
 Identities = 8/47 (17%), Positives = 9/47 (19%), Gaps = 11/47 (23%)

Query: 114 RKRMEMEERDATSRSSFKCPRCLKTFTDL-----------EPCLLVL 149
                   R         CP C      +             C LVL
Sbjct: 6   SIDKRAGRRGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVL 52


>2i52_A Hypothetical protein; structural genomics, unknown function, PSI,
           protein structur initiative; 2.08A {Picrophilus
           torridus} SCOP: d.316.1.1
          Length = 121

 Score = 25.6 bits (56), Expect = 5.7
 Identities = 10/27 (37%), Positives = 13/27 (48%)

Query: 60  KMLRARISTLKNDKIIQTRLRMETGLD 86
           KML A +    N K +   L  + GLD
Sbjct: 85  KMLHAEVLINYNGKKVLGVLNYDEGLD 111


>1uaa_A REP helicase, protein (ATP-dependent DNA helicase REP.); complex
           (helicase/DNA), DNA unwinding, hydrolase/DNA complex;
           HET: DNA; 3.00A {Escherichia coli} SCOP: c.37.1.19
           c.37.1.19
          Length = 673

 Score = 25.6 bits (57), Expect = 8.1
 Identities = 8/33 (24%), Positives = 14/33 (42%), Gaps = 3/33 (9%)

Query: 40  LVRNPCMKEDDICELLKFERKMLRARISTLKND 72
           L++    +     +  K   + L + IS  KND
Sbjct: 116 LLKE-LTEGLIEDD--KVLLQQLISTISNWKND 145


>1yub_A Ermam, rRNA methyltransferase; MLS antibiotics; NMR {Streptococcus
           pneumoniae} SCOP: c.66.1.24
          Length = 245

 Score = 25.2 bits (56), Expect = 9.1
 Identities = 5/47 (10%), Positives = 13/47 (27%)

Query: 33  DSLIIDMLVRNPCMKEDDICELLKFERKMLRARISTLKNDKIIQTRL 79
           +S++I +      + +        F  K +      L         +
Sbjct: 169 NSVLIKLTRHTTDVPDKYWKLYTYFVSKWVNREYRQLFTKNQFHQAM 215


  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
   0.325    0.138    0.414 

Gapped
Lambda     K      H
   0.267   0.0828    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,268,510
Number of extensions: 125022
Number of successful extensions: 573
Number of sequences better than 10.0: 1
Number of HSP's gapped: 571
Number of HSP's successfully gapped: 21
Length of query: 157
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 71
Effective length of database: 4,300,587
Effective search space: 305341677
Effective search space used: 305341677
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.0 bits)