RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4041
         (162 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 = 31.7 bits (71), Expect = 0.11
 Identities = 21/165 (12%), Positives = 35/165 (21%), Gaps = 64/165 (38%)

Query: 1   MFA-FSGDYLCASISCATTVLMWMCDKPEVV--IMYQVGEDKFVSYCMNQKTEKPVLSG- 56
             + F      A I      L+W       V  ++     +K   Y + +K  K      
Sbjct: 377 RLSVFPPS---AHIPTILLSLIWFDVIKSDVMVVV-----NKLHKYSLVEKQPKESTISI 428

Query: 57  ----QRIKTRKRDEKE-------------KYDPAGF-----RDYILS--G---------- 82
                 +K +  +E                +D           Y  S  G          
Sbjct: 429 PSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIPPYLDQYFYSHIGHHLKNIEHPE 488

Query: 83  ------------------LNAAGTDLEAVSKFLDIAGSKVDYRRY 109
                             +    T   A    L+       Y+ Y
Sbjct: 489 RMTLFRMVFLDFRFLEQKIRHDSTAWNASGSILNTLQQLKFYKPY 533


>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 = 30.4 bits (68), Expect = 0.25
 Identities = 19/105 (18%), Positives = 32/105 (30%), Gaps = 32/105 (30%)

Query: 87   GTDL----EAVSKFLDIAGSKVDYRRYGEALFDI---------LIAGGLLGKTLDPTTRA 133
            G DL    +A     + A        YG ++ DI         +  GG  GK +      
Sbjct: 1632 GMDLYKTSKAAQDVWNRA-DNHFKDTYGFSILDIVINNPVNLTIHFGGEKGKRI--RENY 1688

Query: 134  GVMVCRIC----------------KTTACIFEAQEDMQSLKNFEQ 162
              M+                     +T+  F +++ + S   F Q
Sbjct: 1689 SAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQ 1733



 Score = 30.0 bits (67), Expect = 0.42
 Identities = 6/26 (23%), Positives = 12/26 (46%), Gaps = 3/26 (11%)

Query: 78   YILSGLNAAGTDLEAVSKFLDIAGSK 103
            Y+ +G   A   L+ V+  L+    +
Sbjct: 1853 YVAAGDLRA---LDTVTNVLNFIKLQ 1875


>2pt7_A CAG-ALFA; ATPase, protein-protein complex, type IV secretion,
           hydrolas binding complex; 2.40A {Helicobacter pylori}
           SCOP: c.37.1.11 PDB: 1nly_A* 1nlz_A 1opx_A* 1g6o_A
          Length = 330

 Score = 27.7 bits (62), Expect = 1.6
 Identities = 8/66 (12%), Positives = 17/66 (25%), Gaps = 12/66 (18%)

Query: 62  RKRDEKEKYDPAGFRDYILSGLNAAGTDLEAVSKFLDIAGSKVDYRRYGEALFDILIAGG 121
             R             +   G      + E     +      +   +      ++++ GG
Sbjct: 131 SIR--IPSKTTYPHSFFEEQGFYNLLDNKEQAISAIKDG---IAIGK------NVIVCGG 179

Query: 122 L-LGKT 126
              GKT
Sbjct: 180 TGSGKT 185


>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
           vesicle, membrane, Ca structural protein; 7.94A {Bos
           taurus}
          Length = 190

 Score = 27.0 bits (59), Expect = 2.3
 Identities = 11/57 (19%), Positives = 20/57 (35%), Gaps = 19/57 (33%)

Query: 57  QRIKTRKRDEKEKYDPAGFRDYILSGLNAAGTDLEAVSKFLDIAGSKVDYRRYGEAL 113
           QR + ++ D   K     +R+        A  DLE   ++          +R  E +
Sbjct: 94  QRKRLQELDAASKVMEQEWRE-------KAKKDLE---EW---------NQRQSEQV 131


>2ocg_A Valacyclovir hydrolase; alpha beta hydrolase fold; 1.75A {Homo
           sapiens} PDB: 2oci_A* 2ock_A 2ocl_A
          Length = 254

 Score = 26.9 bits (60), Expect = 3.1
 Identities = 9/31 (29%), Positives = 18/31 (58%)

Query: 94  SKFLDIAGSKVDYRRYGEALFDILIAGGLLG 124
           S  + + G ++ Y++ GE    +L+  G+LG
Sbjct: 4   SAKVAVNGVQLHYQQTGEGDHAVLLLPGMLG 34


>3a69_A Flagellar HOOK protein FLGE; the bacterial flagellar motor,
          universal joint, bacterial flagellum, motor protein;
          7.10A {Salmonella enterica subsp}
          Length = 402

 Score = 26.4 bits (58), Expect = 5.6
 Identities = 8/15 (53%), Positives = 12/15 (80%)

Query: 80 LSGLNAAGTDLEAVS 94
          +SGLNAA T+L+ + 
Sbjct: 6  VSGLNAAATNLDVIG 20


  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    0.410 

Gapped
Lambda     K      H
   0.267   0.0501    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,452,939
Number of extensions: 142301
Number of successful extensions: 192
Number of sequences better than 10.0: 1
Number of HSP's gapped: 192
Number of HSP's successfully gapped: 10
Length of query: 162
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 76
Effective length of database: 4,300,587
Effective search space: 326844612
Effective search space used: 326844612
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: 53 (24.7 bits)