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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-U01748-1
Contig ID Contig-U01748-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U01748-1 (Contig-U01748-1Q) /CSM_Contig/Contig-U01748-1Q.Seq.d
CACTCTGTCCAACTTCACCACCAACAACACCTACTGATATTAAATTAAAA
AAACCAACAAAATCAATAAAAACAAAAAATAAAAAATGTCATACTAAAAA
AGAAAAAAAAAAAAAAAAAGAAAAAAGAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAGAAAAAAAAAAAAGAAA
Gap no gap
Contig length 174
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 U01748
List of clone(s) 

est1=SSG431Z,1,175
Translated Amino Acid sequence 
LCPTSPPTTPTDIKLKKPTKSIKTKNKKCHTKKEKKKKKEKRKKKKKKKKKKKKKKE
Translated Amino Acid sequence (All Frames) 
Frame A:
hsvqlhhqqhlliln*knqqnq*kqkiknvilkkkkkkkkkkekkkkkkkkkrkkkkk


Frame B:
tlsnfttnnty*y*ikktnkinknkk*kmsy*krkkkkkrkkkkkkkkkkkkekkkr


Frame C:
LCPTSPPTTPTDIKLKKPTKSIKTKNKKCHTKKEKKKKKEKRKKKKKKKKKKKKKKE
own update 2004. 6. 7
Homology vs CSM-cDNA 
Query= Contig-U01748-1 (Contig-U01748-1Q)
/CSM_Contig/Contig-U01748-1Q.Seq.d
         (174 letters)

Database: CSM
           8361 sequences; 7,895,291 total letters


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U01748-1 (Contig-U01748-1Q) /CSM_Contig/Conti...    80  1e-15
Contig-U13988-1 (Contig-U13988-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U11196-1 (Contig-U11196-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U05635-1 (Contig-U05635-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U02182-1 (Contig-U02182-1Q) /CSM_Contig/Conti...    34  0.063
Contig-U12428-1 (Contig-U12428-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U11846-1 (Contig-U11846-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U09192-1 (Contig-U09192-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U11578-1 (Contig-U11578-1Q) /CSM_Contig/Conti...    28  3.9

>Contig-U01748-1 (Contig-U01748-1Q) /CSM_Contig/Contig-U01748-1Q.Seq.d
          Length = 174

 Score = 79.8 bits (40), Expect = 1e-15
 Identities = 40/40 (100%)
 Strand = Plus / Plus

                                                  
Query: 1  cactctgtccaacttcaccaccaacaacacctactgatat 40
          ||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  cactctgtccaacttcaccaccaacaacacctactgatat 40


>Contig-U13988-1 (Contig-U13988-1Q) /CSM_Contig/Contig-U13988-1Q.Seq.d
          Length = 1297

 Score = 34.2 bits (17), Expect = 0.063
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 13   cttcaccaccaacaaca 29
            |||||||||||||||||
Sbjct: 1034 cttcaccaccaacaaca 1050


>Contig-U11196-1 (Contig-U11196-1Q) /CSM_Contig/Contig-U11196-1Q.Seq.d
          Length = 2477

 Score = 34.2 bits (17), Expect = 0.063
 Identities = 20/21 (95%)
 Strand = Plus / Plus

                                
Query: 9   ccaacttcaccaccaacaaca 29
           |||||| ||||||||||||||
Sbjct: 618 ccaactacaccaccaacaaca 638


  Database: CSM
    Posted date:  Jun 7, 2004  8:33 AM
  Number of letters in database: 7,895,291
  Number of sequences in database:  8361
  
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: 909
Number of Sequences: 8361
Number of extensions: 909
Number of successful extensions: 348
Number of sequences better than 10.0: 79
length of query: 174
length of database: 7,895,291
effective HSP length: 15
effective length of query: 159
effective length of database: 7,769,876
effective search space: 1235410284
effective search space used: 1235410284
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 2009. 5. 6
Homology vs DNA 
Query= Contig-U01748-1 (Contig-U01748-1Q) /CSM_Contig/Contig-U01748-1Q.Seq.d
         (174 letters)

Database: ddbj_A
           102,105,510 sequences; 101,790,757,118 total letters

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

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

(C94119) Dictyostelium discoideum slug cDNA, clone SSG431.         82   7e-12  1
(CU629258) Theobroma cacao, mRNA sequence (KZ0ABB15YI14FM1).       42   6.3    1
(CU527160) Theobroma cacao, mRNA sequence (KZ0ACAA1YD06FM1).       42   6.3    1
(CU519822) Theobroma cacao, mRNA sequence (KZ0ABH7YE01FM1).        42   6.3    1
(CU515873) Theobroma cacao, mRNA sequence (KZ0ABF8YO18FM1).        42   6.3    1
(CU486959) Theobroma cacao, mRNA sequence (KZ0ACAC5YK20FM1).       42   6.3    1
(CU486935) Theobroma cacao, mRNA sequence (KZ0ACAC5YC17FM1).       42   6.3    1

>(C94119) Dictyostelium discoideum slug cDNA, clone SSG431.
          Length = 175

 Score = 81.8 bits (41), Expect = 7e-12
 Identities = 41/41 (100%)
 Strand = Plus / Plus


Query: 1  cactctgtccaacttcaccaccaacaacacctactgatatt 41
          |||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  cactctgtccaacttcaccaccaacaacacctactgatatt 41

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 41,092,539
Number of extensions: 2333859
Number of successful extensions: 627204
Number of sequences better than 10.0: 7
Length of query: 174
Length of database: 101,790,757,118
Length adjustment: 22
Effective length of query: 152
Effective length of database: 99,544,435,898
Effective search space: 15130754256496
Effective search space used: 15130754256496
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.18
Homology vs Protein 
Query= Contig-U01748-1 (Contig-U01748-1Q) /CSM_Contig/Contig-U01748-1Q.Seq.d
         (174 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 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: 3236559
Number of Hits to DB: 53,235,431
Number of extensions: 193988
Number of successful extensions: 679
Number of sequences better than 10.0: 0
Number of HSP's gapped: 679
Number of HSP's successfully gapped: 0
Length of query: 58
Length of database: 1,051,180,864
Length adjustment: 31
Effective length of query: 27
Effective length of database: 950,847,535
Effective search space: 25672883445
Effective search space used: 25672883445
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: 26 (14.6 bits)
PSORT 

 psg: 0.83  gvh: 0.15  alm: 0.70  top: 0.53  tms: 0.00  mit: 0.26  mip: 0.00
 nuc: 1.79  erl: 0.00  erm: 0.80  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 

	 72.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane

>> prediction for Contig-U01748-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 1
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