RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy1603
         (175 letters)



>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 = 38.5 bits (89), Expect = 8e-04
 Identities = 33/206 (16%), Positives = 64/206 (31%), Gaps = 70/206 (33%)

Query: 25  AYVTPSYAHSAVGSQSQSVVRS---------LDGNSVHSV---YSKAVDTPFSSVRK--- 69
            YV+ S    +   Q   V+           L+GN +H++     +  DT     ++   
Sbjct: 66  GYVS-SLVEPSKVGQFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIK 124

Query: 70  --YDSRV---------SNDAIAYA----HAPVY-------HAPVY----------SAPVV 97
               +R+         SN A+  A    +A +        +   Y             +V
Sbjct: 125 NYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEELRDLYQTYHVLV 184

Query: 98  KSVAPVTYAAAPVLKYAAP--------YPYHAPVVKSIAHPVAYSPVAY--HAPVSA--- 144
                +   +A  L             +     +++ + +P       Y    P+S    
Sbjct: 185 G---DLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLENPSNTPDKDYLLSIPISCPLI 241

Query: 145 GV---APYAVKAP---YSPAAVVSHV 164
           GV   A Y V A    ++P  + S++
Sbjct: 242 GVIQLAHYVVTAKLLGFTPGELRSYL 267



 Score = 33.1 bits (75), Expect = 0.042
 Identities = 39/265 (14%), Positives = 70/265 (26%), Gaps = 106/265 (40%)

Query: 7   ALLTC---LLVAV---QAGDYPSVAYVTPSYAHSAV------GSQSQSVVRSLDGNSVHS 54
                   L+ AV   +   + S  +V+      A+      G +      +       S
Sbjct: 269 GATGHSQGLVTAVAIAETDSWES-FFVS---VRKAITVLFFIGVRCYEAYPNTSLPP--S 322

Query: 55  VYSKAVD------TPFSSVRKYDSRVSNDAIAY--AHAPVY---HAPVYSAP---VVKSV 100
           +   +++      +P  S+         D +    +H P        + +     VV S 
Sbjct: 323 ILEDSLENNEGVPSPMLSISNLTQEQVQDYVNKTNSHLPAGKQVEISLVNGAKNLVV-SG 381

Query: 101 APVT-YAAAPVL-KYAA---------PY----------------PYH----APVVKSIAH 129
            P + Y     L K  A         P+                P+H     P    I  
Sbjct: 382 PPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVASPFHSHLLVPASDLINK 441

Query: 130 PVAYSPVAYHA-----PV------------SAGVAPYAVKA--------PYSPAAVVSHV 164
            +  + V+++A     PV            S  ++   V            +     +H+
Sbjct: 442 DLVKNNVSFNAKDIQIPVYDTFDGSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHI 501

Query: 165 -DF----------------DGYGVH 172
            DF                DG GV 
Sbjct: 502 LDFGPGGASGLGVLTHRNKDGTGVR 526


>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
           interaction, metal-binding, nucleus, receptor,
           transcription, transcription regulation, zinc-FIN
           activator; HET: DNA REA BRL; 3.10A {Homo sapiens} PDB:
           3dzu_A* 3e00_A*
          Length = 467

 Score = 27.8 bits (61), Expect = 2.1
 Identities = 16/77 (20%), Positives = 27/77 (35%), Gaps = 6/77 (7%)

Query: 87  YHAPVYSAPVVKSVAPVTYAAAPVLKYAAPYPYHAPVVKSIAHPVAYSPVAYHAPVSAGV 146
           +H  V     + S    +   +P           AP +     P   SP   H+P+S   
Sbjct: 5   HHHHVDDDDKMFSTQVNSSLTSP----TGRGSMAAPSLHPSLGPGIGSPGQLHSPISTLS 60

Query: 147 APYAVKAPYSPAAVVSH 163
           +P  +     P +V+S 
Sbjct: 61  SP--INGMGPPFSVISS 75


>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding,
           complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A
           {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A*
          Length = 388

 Score = 25.7 bits (55), Expect = 9.3
 Identities = 9/92 (9%), Positives = 25/92 (27%)

Query: 36  VGSQSQSVVRSLDGNSVHSVYSKAVDTPFSSVRKYDSRVSNDAIAYAHAPVYHAPVYSAP 95
              + +S  + + G +       ++      +++ +               Y +  Y + 
Sbjct: 39  RHCKEESKYKDIYGKNCAPQKFPSMKDARDWMKRMEDIGLEALGMNDFKLAYISDTYGSE 98

Query: 96  VVKSVAPVTYAAAPVLKYAAPYPYHAPVVKSI 127
           +V     V  A   +      +P        I
Sbjct: 99  IVYDRKFVRVANCDIEVTGDKFPDPMKAEYEI 130


  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
   0.318    0.129    0.382 

Gapped
Lambda     K      H
   0.267   0.0682    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,593,292
Number of extensions: 142491
Number of successful extensions: 256
Number of sequences better than 10.0: 1
Number of HSP's gapped: 256
Number of HSP's successfully gapped: 13
Length of query: 175
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 88
Effective length of database: 4,272,666
Effective search space: 375994608
Effective search space used: 375994608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (24.7 bits)