RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8635
         (177 letters)



>3fbi_B Mediator of RNA polymerase II transcription subunit 31;
           proline-rich stretches, right-handed four-helix bundle,
           protein-protein complex; 2.80A {Saccharomyces
           cerevisiae} PDB: 3fbn_B
          Length = 130

 Score =  139 bits (351), Expect = 4e-43
 Identities = 34/109 (31%), Positives = 55/109 (50%), Gaps = 1/109 (0%)

Query: 8   ETEDQQRLRFQIELEFIQCLANPNYLNFL-AQRGYLKDEAFVNYLKYLLYWKEPQYAKYL 66
             ++    RF++ELEFIQ LAN  Y+ +L  Q+   K   F NYLKYL YW  P Y++ +
Sbjct: 17  SDQNPLPTRFEVELEFIQSLANIQYVTYLLTQQQIWKSPNFKNYLKYLEYWCNPPYSQCI 76

Query: 67  KYPMCLYFLDLLQYEHFRREIVNSQCAKFIDDQQVLLWQHYTRKRTKLL 115
            YP CL+ L LL        +      + +D+   ++     +   +++
Sbjct: 77  VYPNCLFILKLLNGFMESAIVNEDGLLEGLDELPKIIQLQGPQWMNEMV 125


>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 = 37.1 bits (85), Expect = 0.002
 Identities = 34/257 (13%), Positives = 61/257 (23%), Gaps = 99/257 (38%)

Query: 1   MANKGGPET--EDQQRLRFQIELEFIQCLANPNYLNFLAQRGYLKDEAFVNYLKYLLYWK 58
           + N   PET  E  Q+L +QI+  +          +  +    L+  +    L+ LL  K
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTS-------RSDHSSNIKLRIHSIQAELRRLLKSK 241

Query: 59  EPQYAKYLKYPMCLYFLD----------------------------LLQYEHFRREIVNS 90
                    Y  CL  L                              L         ++ 
Sbjct: 242 --------PYENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDH 293

Query: 91  QCAKFIDDQQVLLWQHYTRKRTKLL-NEAAQNN---ISGAPTMERR-------------- 132
                  D+   L   Y   R + L  E    N   +S      R               
Sbjct: 294 HSMTLTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCD 353

Query: 133 ----------SNLSPNDIQPR-------------PEEVWTVLWGPPIN------------ 157
                     + L P + +               P  + +++W   I             
Sbjct: 354 KLTTIIESSLNVLEPAEYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHK 413

Query: 158 -CLLTTSSPSNVLNLHD 173
             L+      + +++  
Sbjct: 414 YSLVEKQPKESTISIPS 430


>2g5g_X Putative lipoprotein; cofacial heme, tyrosine ligand, dimer,
           transport protein; HET: HEM; 1.90A {Campylobacter jejuni
           subsp} SCOP: c.150.1.1
          Length = 268

 Score = 26.2 bits (57), Expect = 6.5
 Identities = 10/57 (17%), Positives = 20/57 (35%)

Query: 12  QQRLRFQIELEFIQCLANPNYLNFLAQRGYLKDEAFVNYLKYLLYWKEPQYAKYLKY 68
            Q + F + LE +      +       +  +K     N L +   WK   Y +++  
Sbjct: 73  SQNINFDVALEMLASTEQNHLDKAFKNKKTIKANELTNALNWDKVWKWKDYEQFVNV 129


>3sv0_A Casein kinase I-like; typical kinase domain fold, cytosol,
           transferase; 2.00A {Oryza sativa japonica group}
          Length = 483

 Score = 25.7 bits (56), Expect = 8.8
 Identities = 16/87 (18%), Positives = 30/87 (34%)

Query: 60  PQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQCAKFIDDQQVLLWQHYTRKRTKLLNEAA 119
            ++A Y  Y   L F D   Y + +R   +    +      V  W     +++++ +   
Sbjct: 246 TEFASYFHYCRSLRFDDKPDYSYLKRLFRDLFIREGFQFDYVFDWTILKYQQSQIASAPP 305

Query: 120 QNNISGAPTMERRSNLSPNDIQPRPEE 146
           +    GA           ND Q   +E
Sbjct: 306 RAVGHGAGPSGLAPPALQNDRQSGVDE 332


>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 = 25.4 bits (55), Expect = 9.4
 Identities = 8/44 (18%), Positives = 16/44 (36%)

Query: 58  KEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQCAKFIDDQQV 101
           + P     L  P C  +   +       ++V + C   + D+ V
Sbjct: 14  RGPNLNIVLTCPECKVYPPKIVERFSEGDVVCALCGLVLSDKLV 57


  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    0.137    0.431 

Gapped
Lambda     K      H
   0.267   0.0585    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,693,941
Number of extensions: 147469
Number of successful extensions: 220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 215
Number of HSP's successfully gapped: 16
Length of query: 177
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 90
Effective length of database: 4,272,666
Effective search space: 384539940
Effective search space used: 384539940
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: 54 (24.9 bits)