RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12002
         (164 letters)



>2xcb_A PCRH, regulatory protein PCRH; protein transport, bacterial toxin,
           type III secretion, protein binding; 1.85A {Pseudomonas
           aeruginosa} PDB: 2xcc_A
          Length = 142

 Score = 27.8 bits (62), Expect = 0.97
 Identities = 24/109 (22%), Positives = 35/109 (32%), Gaps = 20/109 (18%)

Query: 49  LKQAWDLYLTMDTSPESLQILQLIANESYRRAKFWFAFKAFDMLERLEPL-AEYWEGKRG 107
           L     L      S ++L+ L  +    Y+  K+  A K F  L  L+   A Y+ G   
Sbjct: 7   LAMLRGL------SEDTLEQLYALGFNQYQAGKWDDAQKIFQALCMLDHYDARYFLGLGA 60

Query: 108 ACAGLMQMIMA----GKENRLN----VPW---AKC--ALGQYKEAEEMF 143
               L     A         ++          A+C   LG    AE  F
Sbjct: 61  CRQSLGLYEQALQSYSYGALMDINEPRFPFHAAECHLQLGDLDGAESGF 109


>2b1e_A Exocyst complex component EXO70; tethering complex,
           endocytosis/exocytosis complex; 2.00A {Saccharomyces
           cerevisiae} PDB: 2b7m_A 2pfv_A
          Length = 564

 Score = 28.6 bits (63), Expect = 1.0
 Identities = 15/82 (18%), Positives = 30/82 (36%), Gaps = 3/82 (3%)

Query: 39  ESRL-NLVIYHLKQAWDLYLTMDTSPESLQILQLI--ANESYRRAKFWFAFKAFDMLERL 95
           E  L + +     ++    L+   SP      +L     +  R     F F +F+++E +
Sbjct: 194 EKSLVDDLYSQYTESKPHVLSQILSPLISAYAKLFGANLKIVRSNLENFGFFSFELVESI 253

Query: 96  EPLAEYWEGKRGACAGLMQMIM 117
             + +   GK      L+Q   
Sbjct: 254 NDVKKSLRGKELQNYNLLQDCT 275


>3gyz_A Chaperone protein IPGC; asymmetric homodimer, tetratricopeptide
           repeat, TPR, chapero virulence; 2.15A {Shigella
           flexneri} PDB: 3gz1_A 3gz2_A 3ks2_A
          Length = 151

 Score = 27.1 bits (60), Expect = 1.9
 Identities = 16/96 (16%), Positives = 27/96 (28%), Gaps = 14/96 (14%)

Query: 62  SPESLQILQLIANESYRRAKFWFAFKAFDMLERLEPL-AEYWEGKRGACAGLMQMIMA-- 118
             + +  +   A + Y + +   A   F  L   +    +Y  G         Q   A  
Sbjct: 32  PDDMMDDIYSYAYDFYNKGRIEEAEVFFRFLCIYDFYNVDYIMGLAAIYQIKEQFQQAAD 91

Query: 119 --GKENRLN----VPW---AKC--ALGQYKEAEEMF 143
                  L      P     +C   L    +A+E F
Sbjct: 92  LYAVAFALGKNDYTPVFHTGQCQLRLKAPLKAKECF 127


>2ho1_A Type 4 fimbrial biogenesis protein PILF; type IV pilus biogenesis,
           TPR, superhelix, protein binding; HET: MSE; 2.00A
           {Pseudomonas aeruginosa} PDB: 2fi7_A
          Length = 252

 Score = 27.2 bits (61), Expect = 2.4
 Identities = 5/28 (17%), Positives = 10/28 (35%)

Query: 128 WAKCALGQYKEAEEMFLLVQNEGLKNDY 155
                  +Y+EA +  L    + L  + 
Sbjct: 113 GFLYEQKRYEEAYQRLLEASQDTLYPER 140


>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 = 27.5 bits (60), Expect = 2.9
 Identities = 28/174 (16%), Positives = 50/174 (28%), Gaps = 46/174 (26%)

Query: 26  ALQVLPPLIDVIPESRLNLVIYHLKQAWDLYLTMDTSP------ESLQILQ-LIANESYR 78
            L   P  + +I ES     I      WD +  ++          SL +L+     + + 
Sbjct: 322 VLTTNPRRLSIIAES-----IRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFD 376

Query: 79  R---------------AKFWFAFKAFD---MLERLEP--LAEYWEGKRGACAGLMQMIMA 118
           R               +  WF     D   ++ +L    L E    K      +  + + 
Sbjct: 377 RLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVEKQ-PKESTI-SIPSIYLE 434

Query: 119 GKENRLNVPWA-KCALGQYKEAEEMFLLVQNEGL---KND---YVYIS-HLTKC 164
            K    N     +  +  Y   +       ++ L     D   Y +I  HL   
Sbjct: 435 LKVKLENEYALHRSIVDHYNIPKT----FDSDDLIPPYLDQYFYSHIGHHLKNI 484



 Score = 26.0 bits (56), Expect = 8.3
 Identities = 14/105 (13%), Positives = 25/105 (23%), Gaps = 30/105 (28%)

Query: 61  TSPESLQILQLIANESYRRAKFWFAFKAFDMLERLEPLAEYWEGKRGACAG---LMQMIM 117
           T  E   +L           K +   +  D+     P        R         + +I 
Sbjct: 299 TPDEVKSLL----------LK-YLDCRPQDL-----P--------REVLTTNPRRLSIIA 334

Query: 118 AGKENRLNV--PWAKCALGQYKEAEEMFLLVQNEG-LKNDYVYIS 159
               + L     W      +     E  L V      +  +  +S
Sbjct: 335 ESIRDGLATWDNWKHVNCDKLTTIIESSLNVLEPAEYRKMFDRLS 379


>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase,
           nucleotidyltransferase, transcription, transferase;
           11.20A {Escherichia coli} PDB: 3iyd_D*
          Length = 1407

 Score = 27.2 bits (61), Expect = 3.4
 Identities = 14/76 (18%), Positives = 32/76 (42%), Gaps = 14/76 (18%)

Query: 37  IPESRLNLVIYHLKQAWDLYLTMDTSPESLQILQLIANESYRRA--KFWFAFKAF----- 89
           +P   +  V+Y     ++ Y+ ++    +L+  Q++  E Y  A  +F   F A      
Sbjct: 130 MPLRDIERVLY-----FESYVVIEGGMTNLERQQILTEEQYLDALEEFGDEFDAKMGAEA 184

Query: 90  --DMLERLEPLAEYWE 103
              +L+ ++   E  +
Sbjct: 185 IQALLKSMDLEQECEQ 200


  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    0.138    0.428 

Gapped
Lambda     K      H
   0.267   0.0749    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,513,795
Number of extensions: 140693
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 390
Number of HSP's successfully gapped: 13
Length of query: 164
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 78
Effective length of database: 4,300,587
Effective search space: 335445786
Effective search space used: 335445786
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: 53 (24.2 bits)