RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13113
         (286 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 = 37.5 bits (86), Expect = 0.005
 Identities = 24/114 (21%), Positives = 41/114 (35%), Gaps = 29/114 (25%)

Query: 130 EIYDVVASWPGSTHDSRIF-----QNSRVYSRFDRREIRGLLLGDIGYAQNEFTFTPVRN 184
           EI  ++ S    +   R+F     +   +  +F    +  +L   I Y   +F  +P++ 
Sbjct: 50  EIDHIIMSKDAVSGTLRLFWTLLSKQEEMVQKF----VEEVL--RINY---KFLMSPIKT 100

Query: 185 -PITPTPSQVAYNAAQIRTRNS--------VERLFGVLKRRFACLRKKLAN-QP 228
               P+     Y   + R  N         V RL   LK     LR+ L   +P
Sbjct: 101 EQRQPSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLK-----LRQALLELRP 149



 Score = 31.7 bits (71), Expect = 0.32
 Identities = 44/326 (13%), Positives = 88/326 (26%), Gaps = 113/326 (34%)

Query: 2   VLDSNDARGVIHSPVV-------KLLAVLRFYATGNFQIDSEDYHDISQSTICRLVAKVS 54
           VL   +   V ++          K+L   RF    +F   +   H         L     
Sbjct: 249 VLL--N---VQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 55  EEL-AKCHQQWIHF-PEDLQTAKNQFSGIAGFPRVVVGCIDGTHVPIELPSIENGEHYRN 112
           + L  K    ++   P+DL             PR V+        P  L  I   E  R+
Sbjct: 304 KSLLLK----YLDCRPQDL-------------PREVLTTN-----PRRLSII--AESIRD 339

Query: 113 RKHFYSINVQVIGGPNLEIYDVVASWPGSTHD--SRIFQNSRVYSRFDRREIRGLLLGDI 170
                        G           W     D  + I ++S   +  +  E R +     
Sbjct: 340 -------------GLATWDN-----WKHVNCDKLTTIIESS--LNVLEPAEYRKM----- 374

Query: 171 GYAQNEFTFTPVRNPITPTPSQVAYNAAQIRTRNSVERLFGVLKRRFA------CLRKKL 224
            +  +  +  P    I   P+ +            +  ++  + +           +  L
Sbjct: 375 -F--DRLSVFPPSAHI---PTIL------------LSLIWFDVIKSDVMVVVNKLHKYSL 416

Query: 225 ANQ---PTTCS----HIITAC-----AVLHNIAIARREAPP--PENNELPVNV------- 263
             +    +T S    ++           LH   +     P     ++ +P  +       
Sbjct: 417 VEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSH 476

Query: 264 ---HIRDADDNRLGAAVREAFINEHF 286
              H+++ +        R  F++  F
Sbjct: 477 IGHHLKNIEHPERMTLFRMVFLDFRF 502


>3mfx_A Sensory BOX/ggdef family protein; alpha-beta protein, structural
           genomics, PSI-2, protein structure initiative; 2.40A
           {Shewanella oneidensis}
          Length = 129

 Score = 26.6 bits (59), Expect = 4.7
 Identities = 7/37 (18%), Positives = 11/37 (29%), Gaps = 1/37 (2%)

Query: 66  HFPEDLQTAKNQFSGIAGFPRVVVG-CIDGTHVPIEL 101
               D+Q   N    +    +     C  G    +EL
Sbjct: 67  LLSHDVQLGTNCGQPVQHPAQETTLICASGKAKDVEL 103


>3brd_A LIN-12 and GLP-1 phenotype protein 1, isoform A; protein-DNA
           complex, signaling, transcription, notch; HET: DNA;
           2.21A {Caenorhabditis elegans} SCOP: b.1.18.1 b.2.5.8
           b.42.7.1 PDB: 2fo1_A 1ttu_A* 3brf_A*
          Length = 477

 Score = 27.5 bits (60), Expect = 5.3
 Identities = 9/25 (36%), Positives = 12/25 (48%), Gaps = 4/25 (16%)

Query: 170 IGYAQNEFTF----TPVRNPITPTP 190
           I   + E+ F      V NPI+P P
Sbjct: 353 ISTDKAEYRFFEAMGQVANPISPCP 377


>2y1h_A Putative deoxyribonuclease tatdn3; hydrolase; 2.50A {Homo sapiens}
          Length = 272

 Score = 27.5 bits (62), Expect = 5.4
 Identities = 11/27 (40%), Positives = 13/27 (48%), Gaps = 7/27 (25%)

Query: 244 IAIARREAPPPENNELPVNVHIRDADD 270
           I +A+R         LPVNVH R A  
Sbjct: 132 IQLAKRL-------NLPVNVHSRSAGR 151


>3bhw_A Uncharacterized protein; structural genomics, unknown function,
           PSI-2, protein struct initiative; 1.50A
           {Magnetospirillum magneticum}
          Length = 209

 Score = 26.9 bits (59), Expect = 6.8
 Identities = 10/53 (18%), Positives = 22/53 (41%), Gaps = 5/53 (9%)

Query: 196 NAAQIRTRNSVERLFGVLKRRFAC----LRKKLANQPT-TCSHIITACAVLHN 243
           N  Q R+  + +R   +++ R       L + + +  T      + A A+ H+
Sbjct: 46  NVLQRRSPGTAKRQSSLMRNRLETMGPELWQMVRDGSTQVAIQAVFAAAIKHS 98


>3gg7_A Uncharacterized metalloprotein; structural genomics, unknown
           function, plasmid, PSI-2, protein structure initiative;
           1.50A {Deinococcus radiodurans}
          Length = 254

 Score = 26.7 bits (60), Expect = 7.3
 Identities = 4/29 (13%), Positives = 9/29 (31%), Gaps = 6/29 (20%)

Query: 242 HNIAIARREAPPPENNELPVNVHIRDADD 270
           H +                +++H R A+ 
Sbjct: 108 HILRRCEDH------GGRILSIHSRRAES 130


>1zzm_A Putative deoxyribonuclease YJJV; hydrolaze, zinc, PEG, structural
           genomics, PSI; HET: P33; 1.80A {Escherichia coli} SCOP:
           c.1.9.12
          Length = 259

 Score = 26.3 bits (59), Expect = 10.0
 Identities = 8/27 (29%), Positives = 13/27 (48%), Gaps = 7/27 (25%)

Query: 244 IAIARREAPPPENNELPVNVHIRDADD 270
           + +A+R        +LPV +H R   D
Sbjct: 120 LKLAKR-------YDLPVILHSRRTHD 139


  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
   0.322    0.137    0.418 

Gapped
Lambda     K      H
   0.267   0.0694    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,605,608
Number of extensions: 279422
Number of successful extensions: 594
Number of sequences better than 10.0: 1
Number of HSP's gapped: 591
Number of HSP's successfully gapped: 17
Length of query: 286
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 193
Effective length of database: 4,105,140
Effective search space: 792292020
Effective search space used: 792292020
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 (21.9 bits)
S2: 57 (25.8 bits)