RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy11018
         (121 letters)



>2le3_A Carnitine O-palmitoyltransferase 1, liver isoform; membrane
          protein, amphiphilic structure, membrane-protein
          interaction, structural switch; NMR {Homo sapiens}
          Length = 42

 Score = 78.9 bits (194), Expect = 3e-21
 Identities = 21/42 (50%), Positives = 28/42 (66%)

Query: 1  MAEAHSAVAFSFRITHEGWDVNFDREVLHLVWNSGVRSWKKR 42
          MAEAH AVAF F +T +G D+    E L  ++ SG+ SWKK+
Sbjct: 1  MAEAHQAVAFQFTVTPDGIDLRLSHEALRQIYLSGLHSWKKK 42


>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 = 36.2 bits (83), Expect = 0.001
 Identities = 22/124 (17%), Positives = 35/124 (28%), Gaps = 27/124 (21%)

Query: 2    AEAHSAVAFSFRITHEGWDVNFDREVLHLVWNSGVRSWKKRLARFKRLKYRTGNFSAYFS 61
            A+ H    + F I     D+  +  V   +   G +   KR+    R  Y    F     
Sbjct: 1649 ADNHFKDTYGFSIL----DIVINNPVNLTIHFGGEKG--KRI----RENYSAMIFETIVD 1698

Query: 62   LGPVLKRVFG--TEFFPSAIVVPP--------VTQPFHCVQIRLFTTGDTITTVPLRADT 111
                 +++F    E   S               TQP       L           L++  
Sbjct: 1699 GKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQP------ALTLMEKAAFED-LKSKG 1751

Query: 112  LVPP 115
            L+P 
Sbjct: 1752 LIPA 1755



 Score = 33.5 bits (76), Expect = 0.011
 Identities = 8/24 (33%), Positives = 8/24 (33%), Gaps = 7/24 (29%)

Query: 67  KRVFGTEFFPSAIVVPPVTQPFHC 90
           K  F   F P       V  PFH 
Sbjct: 413 KLKFSNRFLP-------VASPFHS 429


>1b63_A MUTL; DNA mismatch repair, ATPase; HET: ANP; 1.90A {Escherichia
           coli K12} SCOP: d.14.1.3 d.122.1.2 PDB: 1nhh_A* 1nhi_A*
           1bkn_A 1nhj_A* 1b62_A*
          Length = 333

 Score = 27.0 bits (61), Expect = 1.4
 Identities = 8/45 (17%), Positives = 14/45 (31%), Gaps = 8/45 (17%)

Query: 1   MAEAHSAVAFSFRITHEGWDVNFDREVLHLVWNSGVRSWKKRLAR 45
           +A A   V  +   +H G      + V            ++RL  
Sbjct: 180 IALARFDVTINL--SHNG------KIVRQYRAVPEGGQKERRLGA 216


>2vxe_A CG10686-PA; EDC3, CAR-1, P-bodies, decapping, mRNA decay, LSM
          proteins, translational repression, transcription; NMR
          {Drosophila melanogaster}
          Length = 88

 Score = 26.0 bits (57), Expect = 1.6
 Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 2/35 (5%)

Query: 60 FSLGPVLKRVFGTEFFPSAIVVPPVTQPFHCVQIR 94
           +L  V  R FGTE   +   + P +Q +  +  R
Sbjct: 40 IALSSV--RSFGTEDRDTQFQIAPQSQIYDYILFR 72


>1jqk_A CODH, carbon monoxide dehydrogenase; rossmann fold, oxidoreductase;
           2.80A {Rhodospirillum rubrum} SCOP: e.26.1.2
          Length = 639

 Score = 26.1 bits (57), Expect = 3.3
 Identities = 4/23 (17%), Positives = 10/23 (43%)

Query: 80  VVPPVTQPFHCVQIRLFTTGDTI 102
           ++P + +   C   ++ TT    
Sbjct: 339 IMPSLPRIAECFHTQIITTDKHN 361


>2fb7_A SM-like protein, LSM-14_N (RAP55); DR.13312, BC055387, AAH55387,
          stronGly BENT five-stranded antiparallel beta- sheet,
          structural genomics, PSI; NMR {Danio rerio} SCOP:
          b.38.1.5 PDB: 2vxf_A
          Length = 95

 Score = 25.2 bits (55), Expect = 3.7
 Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 2/35 (5%)

Query: 60 FSLGPVLKRVFGTEFFPSAIVVPPVTQPFHCVQIR 94
           +L  V  R FGTE  P+   + P  + F  +  R
Sbjct: 46 VALAKV--RSFGTEDRPTDRPIAPRDETFEYIIFR 78


>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 = 25.6 bits (55), Expect = 5.8
 Identities = 7/44 (15%), Positives = 13/44 (29%), Gaps = 11/44 (25%)

Query: 20  DVNFDREVLHLVWNSGVRS---------WKKRLA--RFKRLKYR 52
             +    +L L+W   ++S          K  L   + K     
Sbjct: 384 SAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQPKESTIS 427


>3bt7_A TRNA (uracil-5-)-methyltransferase; methyluridine,
           methyltransferase, TRMA, RUMT; HET: 5MU; 2.43A
           {Escherichia coli}
          Length = 369

 Score = 24.9 bits (55), Expect = 7.4
 Identities = 9/27 (33%), Positives = 12/27 (44%), Gaps = 2/27 (7%)

Query: 53  TGNFSAYFSLGPVLKRVFGTEFFPSAI 79
            GNFS   +L     RV  TE    ++
Sbjct: 224 NGNFS--LALARNFDRVLATEIAKPSV 248


>1wg7_A Dedicator of cytokinesis protein 9; pleckstrin homology domain,
          zizimin1, structural genomics, riken structural
          genomics/proteomics initiative; NMR {Homo sapiens}
          SCOP: b.55.1.1
          Length = 150

 Score = 24.6 bits (53), Expect = 7.9
 Identities = 12/53 (22%), Positives = 20/53 (37%), Gaps = 13/53 (24%)

Query: 14 ITHEGWDVNFDREVLH-----LVWNSGVRSWKKRLARFKRLKYRTGNFSAYFS 61
          IT  GW        L+        +  +RS+K+R     +L   + N + Y  
Sbjct: 18 ITKHGW--------LYKGNMNSAISVTMRSFKRRFFHLIQLGDGSYNLNFYKD 62


  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
   0.327    0.139    0.451 

Gapped
Lambda     K      H
   0.267   0.0596    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,975,377
Number of extensions: 106428
Number of successful extensions: 241
Number of sequences better than 10.0: 1
Number of HSP's gapped: 240
Number of HSP's successfully gapped: 12
Length of query: 121
Length of database: 6,701,793
Length adjustment: 82
Effective length of query: 39
Effective length of database: 4,412,271
Effective search space: 172078569
Effective search space used: 172078569
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 (23.7 bits)