RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3908
         (170 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 = 35.2 bits (80), Expect = 0.007
 Identities = 18/100 (18%), Positives = 33/100 (33%), Gaps = 27/100 (27%)

Query: 66  RQKIIAQAVKLKEGRRFVGVGSRID-----------IPENYPGYFELLSEEGKSMRCCET 114
            QKI        +   +   GS ++           I +N P Y  L++     +   E 
Sbjct: 504 EQKIR------HDSTAWNASGSILNTLQQLKFYKPYICDNDPKYERLVNAILDFLPKIEE 557

Query: 115 VLEISRRKIEAGCLIREAIKGIVAKYDEEGNLQSDGARIV 154
            L  S+       L+R A+        E+  +  +  + V
Sbjct: 558 NLICSKYT----DLLRIALM------AEDEAIFEEAHKQV 587


>3bj5_A Protein disulfide-isomerase; thioredoxin fold, chaperone,
           endoplasmic reticulum, isomeras membrane, redox-active
           center; 2.20A {Homo sapiens}
          Length = 147

 Score = 31.9 bits (72), Expect = 0.043
 Identities = 25/136 (18%), Positives = 49/136 (36%), Gaps = 13/136 (9%)

Query: 19  QYLREFVSKNSLPTVVKIIKGQYGNLGVPTLPSPGLQSTVLLV---SAGKRQKIIAQ--- 72
            +    +  N LP V      ++     P +    +++ +LL    S       ++    
Sbjct: 2   HHHHHHMKHNQLPLV-----IEFTEQTAPKIFGGEIKTHILLFLPKSVSDYDGKLSNFKT 56

Query: 73  -AVKLKEGRRFVGVGSRIDIPENYPGYFELLSEEGKSMRCCETVLEISRRKIEAGCLIRE 131
            A   K    F  + S     +    +F L  EE  ++R      E+++ K E+  L  E
Sbjct: 57  AAESFKGKILFAFIDSDHTDNQRILEFFGLKKEECPAVRLITLEEEMTKYKPESEELTAE 116

Query: 132 AIKGIVAKYDEEGNLQ 147
            I     ++  EG ++
Sbjct: 117 RITEFCHRF-LEGKIK 131


>2kon_A Uncharacterized protein; structural genomics, PSI-2, protein
           structure initiative, northeast structural genomics
           consortium, NESG; NMR {Chromobacterium violaceum}
          Length = 82

 Score = 26.2 bits (57), Expect = 2.1
 Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)

Query: 81  RFVGVGSRIDIPENYPGYFELLSE-EGKSMRCCETVLE 117
           R VGV  R  IP  YP +++L ++ E  S+ C + +++
Sbjct: 31  RKVGVPDRTPIPTTYPEFYDLEADAERVSIACAKIIID 68


>2rkv_A Trichothecene 3-O-acetyltransferase; BAHD superfamily, deoxyniv
           T-2, acetyl COA, fusarium; HET: COA MPO ZBA; 1.60A
           {Gibberella zeae} PDB: 3b2s_A* 3b30_A* 2rkt_A* 2zba_A*
          Length = 451

 Score = 27.2 bits (60), Expect = 2.8
 Identities = 10/62 (16%), Positives = 18/62 (29%), Gaps = 7/62 (11%)

Query: 80  RRFVGVGSRIDIPENYPGYFELLSEEGKSMRCCETVLEISRRKI-EAGCLIREAIKGIVA 138
            R V     + +  NYPG                T+ EI+   +      +R  +     
Sbjct: 290 CRAVDARPAMGVSNNYPGLL------QNMTYHNSTIGEIANESLGATASRLRSELDPASM 343

Query: 139 KY 140
           + 
Sbjct: 344 RQ 345


>2vdj_A Homoserine O-succinyltransferase; methionine biosynthesis,
           amino-acid biosynthesis, homoserine transacetylase,
           homoserine transsuccinylase; 2.00A {Bacillus cereus}
           PDB: 2ghr_A
          Length = 301

 Score = 27.0 bits (59), Expect = 3.2
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 77  KEGRRFVGVGSRIDIPENY 95
           +E  R    G  ID+P+NY
Sbjct: 245 QEYERDRDKGLNIDVPKNY 263


>3ed6_A Betaine aldehyde dehydrogenase; structural genomics, infecti
           deseases, NAD, oxidoreductase, PSI; 1.70A
           {Staphylococcus aureus} PDB: 3fg0_A*
          Length = 520

 Score = 26.4 bits (59), Expect = 6.1
 Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 5/43 (11%)

Query: 60  LVSAGKRQKI---IAQAVKLKEGRRFVGVGSRIDIPENYPGYF 99
           ++S   R KI   +  A    EG      G R D  +   G F
Sbjct: 355 VISTEHRNKIESYMDVAKA--EGATIAVGGKRPDRDDLKDGLF 395


>3cms_A Chymosin B; hydrolase, acid proteinase; 2.00A {Bos taurus} SCOP:
           b.50.1.2 PDB: 4cms_A 1czi_E* 1cms_A
          Length = 323

 Score = 26.1 bits (58), Expect = 6.1
 Identities = 8/29 (27%), Positives = 16/29 (55%)

Query: 12  AKWSDEGQYLREFVSKNSLPTVVKIIKGQ 40
           A  +  G++  +  + + +PTVV  I G+
Sbjct: 238 ATQNQYGEFDIDCDNLSYMPTVVFEINGK 266


>2iw1_A Lipopolysaccharide core biosynthesis protein RFAG; transferase,
           lipopolysaccharide biosynthesis, family GT-4,
           glycosyltransferase, LPS; HET: U2F; 1.5A {Escherichia
           coli} SCOP: c.87.1.8 PDB: 2iv7_A*
          Length = 374

 Score = 25.7 bits (57), Expect = 8.1
 Identities = 14/51 (27%), Positives = 20/51 (39%), Gaps = 1/51 (1%)

Query: 46  VPTLPSPGLQSTVLLVSAG-KRQKIIAQAVKLKEGRRFVGVGSRIDIPENY 95
           + +LP     +T+L V    K +K  A A KL           R D+ E  
Sbjct: 218 LASLPESLRHNTLLFVVGQDKPRKFEALAEKLGVRSNVHFFSGRNDVSELM 268


  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
   0.316    0.136    0.383 

Gapped
Lambda     K      H
   0.267   0.0796    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,641,058
Number of extensions: 159546
Number of successful extensions: 310
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 12
Length of query: 170
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 83
Effective length of database: 4,272,666
Effective search space: 354631278
Effective search space used: 354631278
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 54 (24.5 bits)