RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2291
         (96 letters)



>1ydl_A TFIIH, general transcription factor IIH, polypeptide 5;
          alpha-beta protein, structural genomics, PSI, protein
          structure initiative; 2.30A {Homo sapiens} SCOP:
          d.295.1.1 PDB: 2jnj_A
          Length = 79

 Score = 76.4 bits (188), Expect = 3e-20
 Identities = 29/59 (49%), Positives = 47/59 (79%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDR 95
          D  MKQFLL+LDE+N LG++FIIQD+D+TH+F+ ++++ +L  RV +L+DQ +F +  +
Sbjct: 21 DPAMKQFLLYLDESNALGKKFIIQDIDDTHVFVIAELVNVLQERVGELMDQNAFSLTQK 79


>3dgp_B RNA polymerase II transcription factor B subunit; protein-protein
          complex, beta-alpha-beta spilt, heterodimer, damage,
          DNA excision; 1.80A {Saccharomyces cerevisiae} PDB:
          3dom_B
          Length = 71

 Score = 63.2 bits (154), Expect = 3e-15
 Identities = 13/60 (21%), Positives = 30/60 (50%), Gaps = 3/60 (5%)

Query: 37 DKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDVIELLMTRVDDLLDQISFPINDRD 96
          D  +K  +L +D         ++++LD+THL ++   +E +   ++ LL +  +   D +
Sbjct: 12 DPSIKALILQIDAKM---SDIVLEELDDTHLLVNPSKVEFVKHELNRLLSKNIYNPMDEE 68


>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 = 28.5 bits (63), Expect = 0.30
 Identities = 24/157 (15%), Positives = 47/157 (29%), Gaps = 79/157 (50%)

Query: 12  PM--------KQFLLHLDETNT-----------L--GRR-FII----------------- 32
           PM        +Q   ++++TN+           L  G +  ++                 
Sbjct: 337 PMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVVSGPPQSLYGLNLTLRKA 396

Query: 33  HC----------FSD-KPM--KQFL-----LH---LDETNTLGRRFIIQDLDETHLFIS- 70
                       FS+ K     +FL      H   L   + L    I +DL + ++  + 
Sbjct: 397 KAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDL----INKDLVKNNVSFNA 452

Query: 71  -------------SDVIELLMTRVDDLLDQI-SFPIN 93
                        SD+  L  +  + ++D I   P+ 
Sbjct: 453 KDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVK 489


>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 = 28.3 bits (62), Expect = 0.44
 Identities = 18/87 (20%), Positives = 29/87 (33%), Gaps = 18/87 (20%)

Query: 4   YCNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLHLDETNTLGRRFIIQDLD 63
           + +  D        L +       RR        KP +  LL L           +Q+  
Sbjct: 213 WTSRSD--HSSNIKLRIHSIQAELRRL----LKSKPYENCLLVLLN---------VQNAK 257

Query: 64  ETHLF-ISSDVIELLMTRVDDLLDQIS 89
             + F +S  +  LL TR   + D +S
Sbjct: 258 AWNAFNLSCKI--LLTTRFKQVTDFLS 282



 Score = 26.0 bits (56), Expect = 2.8
 Identities = 15/74 (20%), Positives = 27/74 (36%), Gaps = 10/74 (13%)

Query: 19 HLD-ETNT--LGRRFIIHCFSDKPMKQFLLH--LDETNTLGRRFIIQDLDETHLFISSDV 73
          H+D ET       + I+  F D  +  F      D       + I+   +  H+ +S D 
Sbjct: 6  HMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMP-----KSILSKEEIDHIIMSKDA 60

Query: 74 IELLMTRVDDLLDQ 87
          +   +     LL +
Sbjct: 61 VSGTLRLFWTLLSK 74


>1l3e_B P300 protein; protein-protein complex, transcription; NMR {Homo
          sapiens} SCOP: g.53.1.1 PDB: 1p4q_B 1r8u_B 2ka4_A
          1l8c_A 1u2n_A 1liq_A
          Length = 101

 Score = 24.5 bits (53), Expect = 4.5
 Identities = 11/42 (26%), Positives = 17/42 (40%), Gaps = 3/42 (7%)

Query: 5  CNYVDDKPMKQFLLHLDETNTLGRRFIIHCFSDKPMKQFLLH 46
          CN    + MK  L H+    +     + HC S    +Q + H
Sbjct: 42 CNLPHCRTMKNVLNHMTHCQSGKSCQVAHCAS---SRQIISH 80


>3hhs_A Propo-P2, phenoloxidase subunit 2; alpha helix, beta strand,
           melanin biosynthesis, metal-bindin monooxygenase,
           oxidoreductase, secreted; 1.97A {Manduca sexta}
          Length = 694

 Score = 25.0 bits (54), Expect = 4.9
 Identities = 10/75 (13%), Positives = 27/75 (36%), Gaps = 4/75 (5%)

Query: 18  LHLDETNTLGRRFI----IHCFSDKPMKQFLLHLDETNTLGRRFIIQDLDETHLFISSDV 73
            + +    L  RF     +           +    +   L           +H  ++++V
Sbjct: 39  EYANNGLELNNRFGDEEEVSRKIILKNLDKIPEFPKAKQLPNDADFSLFLPSHQEMANEV 98

Query: 74  IELLMTRVDDLLDQI 88
           I++LM+  ++ L ++
Sbjct: 99  IDVLMSVTENQLQEL 113


>3g9g_A Suppressor of yeast profilin deletion; SYP1, BAR domain, FCH,
           adaptor, endocytosis, phosphoprotein; 2.40A
           {Saccharomyces cerevisiae}
          Length = 287

 Score = 24.7 bits (53), Expect = 6.3
 Identities = 5/29 (17%), Positives = 9/29 (31%)

Query: 60  QDLDETHLFISSDVIELLMTRVDDLLDQI 88
           + +D   L    + +    T   D L   
Sbjct: 212 ETIDYNRLDTLKNCMLRFQTSFSDYLLNT 240


  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
   0.328    0.146    0.435 

Gapped
Lambda     K      H
   0.267   0.0507    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,473,996
Number of extensions: 76661
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 29
Length of query: 96
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 34
Effective length of database: 4,970,691
Effective search space: 169003494
Effective search space used: 169003494
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.9 bits)