RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy8730
         (287 letters)



>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 = 38.7 bits (89), Expect = 0.002
 Identities = 17/105 (16%), Positives = 35/105 (33%), Gaps = 15/105 (14%)

Query: 1   MSRKHNSSDTNYVTSRTYNNSDKTKVHAEKSLYITYLLWLVGGIFGVHHFYLGRDIQGFL 60
               H S   +Y   +T+++ D    + ++     Y    +G     HH       +   
Sbjct: 442 EYALHRSIVDHYNIPKTFDSDDLIPPYLDQ-----YFYSHIG-----HHLKNIEHPERMT 491

Query: 61  WWCTLGGYFGFGWLRDIFHIQNYVADANKDRDYLDKFNHNLRSYK 105
            +  +  +  F +L     I++     N     L+     L+ YK
Sbjct: 492 LFRMV--FLDFRFLEQ--KIRHDSTAWNASGSILNTLQ-QLKFYK 531


>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 = 37.7 bits (87), Expect = 0.005
 Identities = 56/324 (17%), Positives = 87/324 (26%), Gaps = 117/324 (36%)

Query: 30  KSLYITYLLWLVGGIFGVH----------------HFYLGRDIQGFLWWCTLGGYFGFGW 73
           + LY TY + LVG +                     F  G +I                W
Sbjct: 174 RDLYQTYHV-LVGDLIKFSAETLSELIRTTLDAEKVFTQGLNIL--------------EW 218

Query: 74  LRDIFHIQNYVADANKDRDYLD------------KFNH---NLRSYKYPPFSTI-RFTGM 117
           L +             D+DYL             +  H     +   + P        G 
Sbjct: 219 LEN--------PSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGA 270

Query: 118 T-----VVAYLWSTVVSMAIPEEDIGGLPWKYLHFLLPIACALGVWSVGNIGHETGTIWW 172
           T     +V    +  ++     E       K +  L         +    IG        
Sbjct: 271 TGHSQGLVT---AVAIAETDSWESFFVSVRKAITVLF--------F----IG-------- 307

Query: 173 CLAAAYACYPVY----------WYVDESTACTVMVLASALAFDTLSKRWQT--KPKPRKR 220
                Y  YP               +E    + M+  S L  + +           P  +
Sbjct: 308 --VRCYEAYPNTSLPPSILEDSLENNEGVP-SPMLSISNLTQEQVQDYVNKTNSHLPAGK 364

Query: 221 FLRRCLTIGACALLYS----SLWGSYLYF-NAKITDGEGE-EIPLNE---AIHH-F---- 266
            +   L  GA  L+ S    SL+G  L    AK   G  +  IP +E      + F    
Sbjct: 365 QVEISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRFLPVA 424

Query: 267 --FKSPW---WVDLLAVELPRDGV 285
             F S       DL+  +L ++ V
Sbjct: 425 SPFHSHLLVPASDLINKDLVKNNV 448



 Score = 37.0 bits (85), Expect = 0.006
 Identities = 24/157 (15%), Positives = 43/157 (27%), Gaps = 46/157 (29%)

Query: 79  HIQNYVADANKDRDY--------LDKFNHNLRSYKYP--------PFS------TIRFTG 116
            +   ++  N  ++         L   N  LR  K P        PFS      + RF  
Sbjct: 365 QV--EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIPFSERKLKFSNRF-- 420

Query: 117 MTVVA-----YLWSTVVSMAIPEEDIGGLPWKYLHFLLPIACALGVWSVG---NIGHETG 168
           + V +      L      +   +     + +      +P      V+      ++   +G
Sbjct: 421 LPVASPFHSHLL-VPASDLINKDLVKNNVSFNAKDIQIP------VYDTFDGSDLRVLSG 473

Query: 169 TIWWCLAAAYACYPVYWYVDESTACTVMVLASALAFD 205
           +I   +       PV W        T       L F 
Sbjct: 474 SISERIVDCIIRLPVKW-----ETTTQFKATHILDFG 505



 Score = 30.8 bits (69), Expect = 0.57
 Identities = 20/87 (22%), Positives = 29/87 (33%), Gaps = 25/87 (28%)

Query: 208 SKRWQTKPKPRKRFLR-------RCLTIGACALLYSSLWGSYLYFNAKITDGEGEEIPLN 260
           S+R   K K   RFL          L   A  L+   L  + + FNAK          + 
Sbjct: 410 SER---KLKFSNRFLPVASPFHSHLLV-PASDLINKDLVKNNVSFNAK---------DIQ 456

Query: 261 EAIHHFFKSPWWVDL--LAVELPRDGV 285
             ++  F      DL  L+  +    V
Sbjct: 457 IPVYDTFD---GSDLRVLSGSISERIV 480


>3vmt_A Monofunctional glycosyltransferase; transmembrane, bacterial cell
           WALL SYNT membrane; HET: LHI; 2.30A {Staphylococcus
           aureus} PDB: 3vmr_A* 3vms_A 3vmq_A*
          Length = 263

 Score = 27.3 bits (61), Expect = 5.5
 Identities = 10/38 (26%), Positives = 18/38 (47%)

Query: 214 KPKPRKRFLRRCLTIGACALLYSSLWGSYLYFNAKITD 251
           KP  +K+  R  L I    L+  +L+   +YF +   +
Sbjct: 26  KPPKKKKSKRILLKILLTILIIIALFIGIMYFLSTRDN 63


>3owq_A LIN1025 protein; structural genomics, PSI-biology, protein
           structure initiati northeast structural genomics
           consortium, NESG, unknown FUN; 2.61A {Listeria innocua}
           PDB: 3nro_A
          Length = 321

 Score = 27.0 bits (60), Expect = 7.8
 Identities = 5/42 (11%), Positives = 15/42 (35%), Gaps = 1/42 (2%)

Query: 208 SKRWQTKPKPRKRFLRR-CLTIGACALLYSSLWGSYLYFNAK 248
           ++  Q KP    + ++   +T+        +   +  Y   +
Sbjct: 6   TETKQKKPSTFTKVMKIASVTLLGILFFSITGLAAKYYITVQ 47


>3fwm_A Penicillin-binding protein 1B; bacterial cell WALL synthesis,
           antibiotics design, transferase, hydrolase; HET: M0E;
           2.16A {Escherichia coli} PDB: 3fwl_A* 3vma_A*
          Length = 751

 Score = 26.9 bits (60), Expect = 9.3
 Identities = 9/40 (22%), Positives = 19/40 (47%), Gaps = 2/40 (5%)

Query: 212 QTKPKPRKRFLRRCLTIGACALLYSSLWGSYLYFNAKITD 251
             KP+ ++ +L   L +     +  +++G YL  + KI  
Sbjct: 3   HMKPRGKRGWLWLLLKLAIVFAVLIAIYGVYL--DQKIRS 40


  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    0.140    0.480 

Gapped
Lambda     K      H
   0.267   0.0693    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,769,429
Number of extensions: 283596
Number of successful extensions: 630
Number of sequences better than 10.0: 1
Number of HSP's gapped: 628
Number of HSP's successfully gapped: 17
Length of query: 287
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 194
Effective length of database: 4,105,140
Effective search space: 796397160
Effective search space used: 796397160
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: 57 (25.8 bits)