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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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Contig-U10483-1
Contig ID Contig-U10483-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U10483-1 (Contig-U10483-1Q) /CSM_Contig/Contig-U10483-1Q.Seq.d
NNNNNNNNNNATTGNTTTTATCANCCNAAAATNATGAATTAGGNCCNGCN
TNTCANANGAAACNTTTAAANAAACNNGNTCNTCNANGCNAAAAAAAAAC
NATTGNTTTTNAAAATGGNAGACNNANGGNTTTAATGNTTCNACNTAATT
TTTATNAANATATTAAANAATTTNTGNTANAAAAATTTGGNGNCNANATC
NNAAAACCATGATATAGNCCAAAAAAAAAATAAAAAAAAACCAAAATAAT
AATAATATAGAAAAATAATAATAATAATAATAATAATATAGAAAAAAAAA
TAATATAGAAAAAAAAAAGTAAATAAAATAAAAAATATAAAAATGTATTA
TTTATATG
Gap no gap
Contig length 358
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U10483
List of clone(s) 

est1=VFM126Z,1,349
Translated Amino Acid sequence 
XXXLXLSXXNXELGPAXXXKXLXKXXXXXXKKTIXFXNGRXXXLMXXXNFYXXIKXFXXX
KFGXXIXKP*yxpkkk*kktkiiii*knnnnnnnniekkii*kkksk*nkkyknvlfi
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxxfyxpkxmn*xxxxxxnx*xnxxxxakkkxlxxkmxdxxx*xfxxifxxilxnxxx
knlxxxsxnhdixqkknkkkpk***yrkiiiiiiii*kkk*yrkkkvnkiknikmyyly


Frame B:
xxxixfixxkx*irxxxsxetfkxtxssxxkknxxfxkwxtxgfnxst*flxxy*xixxx
kiwxxxxktmi*xkkkikknqnnnniek*******yrkknniekkk*ik*ki*kciiym


Frame C:
XXXLXLSXXNXELGPAXXXKXLXKXXXXXXKKTIXFXNGRXXXLMXXXNFYXXIKXFXXX
KFGXXIXKP*yxpkkk*kktkiiii*knnnnnnnniekkii*kkksk*nkkyknvlfi
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U10483-1 (Contig-U10483-1Q)
/CSM_Contig/Contig-U10483-1Q.Seq.d
         (358 letters)

Database: CSM
           6905 sequences; 5,674,871 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U10483-1 (Contig-U10483-1Q) /CSM_Contig/Conti...   107  8e-24
Contig-U11882-1 (Contig-U11882-1Q) /CSM_Contig/Conti...    28  6.0
Contig-U11699-1 (Contig-U11699-1Q) /CSM_Contig/Conti...    28  6.0
Contig-U11454-1 (Contig-U11454-1Q) /CSM_Contig/Conti...    28  6.0
Contig-U10926-1 (Contig-U10926-1Q) /CSM_Contig/Conti...    28  6.0
Contig-U09858-1 (Contig-U09858-1Q) /CSM_Contig/Conti...    28  6.0
Contig-U08366-1 (Contig-U08366-1Q) /CSM_Contig/Conti...    28  6.0
Contig-U03794-1 (Contig-U03794-1Q) /CSM_Contig/Conti...    28  6.0

>Contig-U10483-1 (Contig-U10483-1Q) /CSM_Contig/Contig-U10483-1Q.Seq.d
          Length = 358

 Score =  107 bits (54), Expect = 8e-24
 Identities = 198/207 (95%)
 Strand = Plus / Plus

                                                                       
Query: 11  attgnttttatcanccnaaaatnatgaattaggnccngcntntcanangaaacntttaaa 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  attgnttttatcanccnaaaatnatgaattaggnccngcntntcanangaaacntttaaa 70

                                                                       
Query: 71  naaacnngntcntcnangcnnnnnnnnnncnattgnttttnaaaatggnagacnnanggn 130
           ||||||||||||||||||||         |||||||||||||||||||||||||||||||
Sbjct: 71  naaacnngntcntcnangcnaaaaaaaaacnattgnttttnaaaatggnagacnnanggn 130

                                                                       
Query: 131 tttaatgnttcnacntaatttttatnaanatattaaanaatttntgntanaaaaatttgg 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 131 tttaatgnttcnacntaatttttatnaanatattaaanaatttntgntanaaaaatttgg 190

                                      
Query: 191 ngncnanatcnnaaaaccatgatatag 217
           |||||||||||||||||||||||||||
Sbjct: 191 ngncnanatcnnaaaaccatgatatag 217


 Score = 30.2 bits (15), Expect = 1.5
 Identities = 15/15 (100%)
 Strand = Plus / Plus

                          
Query: 344 tgtattatttatatg 358
           |||||||||||||||
Sbjct: 344 tgtattatttatatg 358


>Contig-U11882-1 (Contig-U11882-1Q) /CSM_Contig/Contig-U11882-1Q.Seq.d
          Length = 664

 Score = 28.2 bits (14), Expect = 6.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 344 tgtattatttatat 357
           ||||||||||||||
Sbjct: 642 tgtattatttatat 655


>Contig-U11699-1 (Contig-U11699-1Q) /CSM_Contig/Contig-U11699-1Q.Seq.d
          Length = 1372

 Score = 28.2 bits (14), Expect = 6.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 344 tgtattatttatat 357
           ||||||||||||||
Sbjct: 617 tgtattatttatat 604


  Database: CSM
    Posted date:  Jun 9, 2004  7:35 PM
  Number of letters in database: 5,674,871
  Number of sequences in database:  6905
  
Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.37    0.711     1.31 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 5, Extension: 2
Number of Hits to DB: 555
Number of Sequences: 6905
Number of extensions: 555
Number of successful extensions: 31
Number of sequences better than 10.0: 9
length of query: 358
length of database: 5,674,871
effective HSP length: 16
effective length of query: 342
effective length of database: 5,564,391
effective search space: 1903021722
effective search space used: 1903021722
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 14 (28.2 bits)
dna update 2008.11.20
Homology vs DNA 
Query= Contig-U10483-1 (Contig-U10483-1Q) /CSM_Contig/Contig-U10483-1Q.Seq.d
         (358 letters)

Database: ddbj_A
           92,845,959 sequences; 95,242,211,685 total letters

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

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

(BJ434881) Dictyostelium discoideum cDNA clone:ddv25c07, 3' ...   100   9e-30  3

>(BJ434881) Dictyostelium discoideum cDNA clone:ddv25c07, 3' end,
           single read.
          Length = 349

 Score = 99.6 bits (50), Expect(3) = 9e-30
 Identities = 116/116 (100%)
 Strand = Plus / Minus


Query: 102 attgnttttnaaaatggnagacnnanggntttaatgnttcnacntaatttttatnaanat 161
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 258 attgnttttnaaaatggnagacnnanggntttaatgnttcnacntaatttttatnaanat 199


Query: 162 attaaanaatttntgntanaaaaatttggngncnanatcnnaaaaccatgatatag 217
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 198 attaaanaatttntgntanaaaaatttggngncnanatcnnaaaaccatgatatag 143

 Score = 58.0 bits (29), Expect(3) = 9e-30
 Identities = 65/65 (100%)
 Strand = Plus / Minus


Query: 11  attgnttttatcanccnaaaatnatgaattaggnccngcntntcanangaaacntttaaa 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 349 attgnttttatcanccnaaaatnatgaattaggnccngcntntcanangaaacntttaaa 290


Query: 71  naaac 75
           |||||
Sbjct: 289 naaac 285

 Score = 28.2 bits (14), Expect(3) = 9e-30
 Identities = 14/14 (100%)
 Strand = Plus / Minus


Query: 345 gtattatttatatg 358
           ||||||||||||||
Sbjct: 15  gtattatttatatg 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 58,527,894
Number of extensions: 2888184
Number of successful extensions: 56661
Number of sequences better than 10.0: 1
Length of query: 358
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 335
Effective length of database: 93,106,754,628
Effective search space: 31190762800380
Effective search space used: 31190762800380
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.28
Homology vs Protein 
Query= Contig-U10483-1 (Contig-U10483-1Q) /CSM_Contig/Contig-U10483-1Q.Seq.d
         (358 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

 ***** No hits found ******

Lambda     K      H
   0.318    0.134    0.401

Gapped
Lambda     K      H
   0.267   0.0410    0.140

Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 3204285
Number of Hits to DB: 107,713,019
Number of extensions: 7841104
Number of successful extensions: 5
Number of sequences better than 10.0: 0
Number of HSP's gapped: 5
Number of HSP's successfully gapped: 0
Length of query: 119
Length of database: 1,040,966,779
Length adjustment: 85
Effective length of query: 34
Effective length of database: 768,602,554
Effective search space: 26132486836
Effective search space used: 26132486836
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 28 (15.4 bits)
PSORT 

 psg: 0.75  gvh: 0.43  alm: 0.57  top: 0.53  tms: 0.00  mit: 0.24  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.20  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 48.0 %: nuclear
	 28.0 %: cytoplasmic
	 12.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U10483-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 1
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0