RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3140
         (138 letters)



>4a6q_A Histone deacetylase complex subunit SAP18; transcription, splicing,
           RNA metabolism, ubiquitin-like; HET: MSE; 1.50A {Mus
           musculus} PDB: 4a90_A* 2hde_A 4a8x_C
          Length = 143

 Score =  167 bits (423), Expect = 2e-54
 Identities = 68/138 (49%), Positives = 96/138 (69%), Gaps = 2/138 (1%)

Query: 1   MTAIESFVTSIDEKTVDREKTCPLLLRVFT-NFGKHNNVSDFHNG-FPPNQLQIYTWMDA 58
           M   +  +    EK +DREKTCPLLLRVFT N G+H+ + +F  G  P ++LQIYTWMDA
Sbjct: 5   MRVTQEEIKKEPEKPIDREKTCPLLLRVFTTNNGRHHRMDEFSRGNVPSSELQIYTWMDA 64

Query: 59  TLRELTNLIREVNPEAQQRGTCFYFTLLTPERGTSRFHVRDIGQTICGQKGPDDNKTLQQ 118
           TL+ELT+L++EV PEA+++GT F F ++  +     + V++IG T+ G+KG DD+ TLQ 
Sbjct: 65  TLKELTSLVKEVYPEARKKGTHFNFAIVFMDLKRPGYRVKEIGSTMSGRKGTDDSMTLQS 124

Query: 119 CRFIIGDYMDVKILTPKR 136
            +F IGDY+D+ I  P R
Sbjct: 125 QKFQIGDYLDIAITPPNR 142


>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 = 29.6 bits (66), Expect = 0.35
 Identities = 8/50 (16%), Positives = 19/50 (38%), Gaps = 15/50 (30%)

Query: 42  HNGFPPNQLQIY--------TWM----DATLRELTNLIREVN---PEAQQ 76
           +   PP+ L+          + M    + T  ++ + + + N   P  +Q
Sbjct: 316 NTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQ 365


>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 = 28.9 bits (64), Expect = 0.41
 Identities = 11/64 (17%), Positives = 16/64 (25%), Gaps = 22/64 (34%)

Query: 69  EVNPEAQQRGTCFYFTLLTPE-RGTSRFHVRDI--GQTICGQKGPDDNKTLQQCRFIIGD 125
              P      TC       PE +      V     G  +C             C  ++ D
Sbjct: 13  RRGPNLNIVLTC-------PECKVYPPKIVERFSEGDVVCA-----------LCGLVLSD 54

Query: 126 -YMD 128
             +D
Sbjct: 55  KLVD 58


>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 = 0.93
 Identities = 14/87 (16%), Positives = 28/87 (32%), Gaps = 13/87 (14%)

Query: 11 IDEKTVDREKTCPLLLRVFTNFGKHNNVSDFHNGFPPNQLQIYTWMDATLRELTNLIREV 70
          +D +T + +     +L VF           F + F    +Q       +  E+ ++I   
Sbjct: 7  MDFETGEHQYQYKDILSVF--------EDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSK 58

Query: 71 NPEAQQRGTCFYFTLL--TPERGTSRF 95
          +  +        F  L    E    +F
Sbjct: 59 DAVSGTL---RLFWTLLSKQEEMVQKF 82


>2osx_A Endoglycoceramidase II; (alpha/beta)8 (TIM) barrel, hydrolase; HET:
           SIA GAL BGC 16C; 1.10A {Rhodococcus SP} PDB: 2oyk_A*
           2osw_A* 2oyl_A* 2oym_A* 2osy_A*
          Length = 481

 Score = 27.2 bits (59), Expect = 2.0
 Identities = 12/78 (15%), Positives = 25/78 (32%), Gaps = 6/78 (7%)

Query: 2   TAIESFVTSIDEKTVDREKTCPLLLRVFTNFGKHNNVSDF------HNGFPPNQLQIYTW 55
            A ++F  +  +     E        V   F  ++ V  +        G           
Sbjct: 180 RAFDNFWNTTGKHPELVEHYAKAWRAVADRFADNDAVVAYDLMNEPFGGSLQGPAFEAGP 239

Query: 56  MDATLRELTNLIREVNPE 73
           + A  +  T+ IR+V+ +
Sbjct: 240 LAAMYQRTTDAIRQVDQD 257


>2fmd_A Lectin, agglutinin, BMA; legume lectin, beta sandwich,
          protein-carbohydrate complex, sugar binding protein;
          HET: MAN; 1.90A {Bowringia mildbraedii}
          Length = 240

 Score = 25.9 bits (56), Expect = 5.4
 Identities = 10/45 (22%), Positives = 17/45 (37%), Gaps = 5/45 (11%)

Query: 43 NGFPPNQLQIYTWMDATLR-----ELTNLIREVNPEAQQRGTCFY 82
            F   Q  +    DA++      +LT +  + NP+    G   Y
Sbjct: 9  TDFESGQQDLIFQGDASVGSNKALQLTKVDSKGNPQGGSVGRALY 53


>1qmo_A Mannose binding lectin, FRIL; crosslink, hematopoietic
          progenitor, sugar complex; HET: MAN; 3.5A {Dolichos lab
          lab} SCOP: b.29.1.1
          Length = 113

 Score = 25.2 bits (55), Expect = 5.9
 Identities = 12/44 (27%), Positives = 16/44 (36%), Gaps = 4/44 (9%)

Query: 43 NGFPPNQLQIYTWMDATLR----ELTNLIREVNPEAQQRGTCFY 82
            F PNQ  +     AT      ++T L    NP +   G   Y
Sbjct: 9  TKFDPNQEDLIFQGHATSTNNVLQVTKLDSAGNPVSSSAGRVLY 52


>3e1y_E Eukaryotic peptide chain release factor GTP-bindi ERF3A;
           translation termination, peptide release, PTC, P
           biosynthesis, GTP-binding; HET: ATP; 3.80A {Homo
           sapiens}
          Length = 204

 Score = 25.2 bits (56), Expect = 7.4
 Identities = 7/11 (63%), Positives = 9/11 (81%)

Query: 94  RFHVRDIGQTI 104
           RF +RD G+TI
Sbjct: 181 RFTLRDEGKTI 191


  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
   0.323    0.139    0.428 

Gapped
Lambda     K      H
   0.267   0.0590    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,125,787
Number of extensions: 113819
Number of successful extensions: 185
Number of sequences better than 10.0: 1
Number of HSP's gapped: 184
Number of HSP's successfully gapped: 13
Length of query: 138
Length of database: 6,701,793
Length adjustment: 84
Effective length of query: 54
Effective length of database: 4,356,429
Effective search space: 235247166
Effective search space used: 235247166
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 52 (24.1 bits)