NBDC - アーカイブトップ - ヘルプ
データベースの説明 | データ項目の説明 | 利用許諾 | ヘルプ
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
NBDC - LSDB Archive
Description of this DB | Description of data items | Download | License
Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U12850-1
Contig ID Contig-U12850-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12850-1 (Contig-U12850-1Q) /CSM_Contig/Contig-U12850-1Q.Seq.d
NNNNNNNNNNGCNTTAAATTCATTNNCCGNTNAAAATNNGATTGNAAAAN
NTTTTGAANANANAAAATNCANNAAAGCNNTTAGATCNCTTNATTANTTT
CGTTTAAAAATTTGTNNNAAACATGNTNTTGGAATCGCCNAACNTTANNC
NTTTGGNG
Gap no gap
Contig length 158
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 U12850
List of clone(s) 

est1=AHQ823Z,1,149
Translated Amino Acid sequence 
XXXALNSXXXXNXIXKXFEXXKXXKAXRSLXXFRLKICXKHXXGIAXXXXFG
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxxkfixrxkxdxkxf*xxkxxxsx*ixxlxsfknlxxtxxwnrxtlxxw


Frame B:
XXXALNSXXXXNXIXKXFEXXKXXKAXRSLXXFRLKICXKHXXGIAXXXXFG


Frame C:
xxxx*ihxpxkxxlxxxlxxxnxxkxldxxixfv*kfvxnmxlespnxxxlx
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12850-1 (Contig-U12850-1Q)
/CSM_Contig/Contig-U12850-1Q.Seq.d
         (158 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12850-1 (Contig-U12850-1Q) /CSM_Contig/Conti...   105  1e-23
Contig-U13258-1 (Contig-U13258-1Q) /CSM_Contig/Conti...    32  0.16
Contig-U14764-1 (Contig-U14764-1Q) /CSM_Contig/Conti...    28  2.5
Contig-U10902-1 (Contig-U10902-1Q) /CSM_Contig/Conti...    28  2.5
Contig-U14877-1 (Contig-U14877-1Q) /CSM_Contig/Conti...    26  9.9
Contig-U12462-1 (Contig-U12462-1Q) /CSM_Contig/Conti...    26  9.9
Contig-U12064-1 (Contig-U12064-1Q) /CSM_Contig/Conti...    26  9.9
Contig-U11436-1 (Contig-U11436-1Q) /CSM_Contig/Conti...    26  9.9
Contig-U11249-1 (Contig-U11249-1Q) /CSM_Contig/Conti...    26  9.9

>Contig-U12850-1 (Contig-U12850-1Q) /CSM_Contig/Contig-U12850-1Q.Seq.d
          Length = 158

 Score =  105 bits (53), Expect = 1e-23
 Identities = 134/134 (100%)
 Strand = Plus / Plus

                                                                       
Query: 14  ttaaattcattnnccgntnaaaatnngattgnaaaannttttgaanananaaaatncann 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 14  ttaaattcattnnccgntnaaaatnngattgnaaaannttttgaanananaaaatncann 73

                                                                       
Query: 74  aaagcnnttagatcncttnattantttcgtttaaaaatttgtnnnaaacatgntnttgga 133
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 74  aaagcnnttagatcncttnattantttcgtttaaaaatttgtnnnaaacatgntnttgga 133

                         
Query: 134 atcgccnaacntta 147
           ||||||||||||||
Sbjct: 134 atcgccnaacntta 147


>Contig-U13258-1 (Contig-U13258-1Q) /CSM_Contig/Contig-U13258-1Q.Seq.d
          Length = 137

 Score = 32.2 bits (16), Expect = 0.16
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 98  tttcgtttaaaaattt 113
           ||||||||||||||||
Sbjct: 113 tttcgtttaaaaattt 128


>Contig-U14764-1 (Contig-U14764-1Q) /CSM_Contig/Contig-U14764-1Q.Seq.d
          Length = 1026

 Score = 28.2 bits (14), Expect = 2.5
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 100 tcgtttaaaaattt 113
           ||||||||||||||
Sbjct: 839 tcgtttaaaaattt 852


  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: 564
Number of Sequences: 6905
Number of extensions: 564
Number of successful extensions: 66
Number of sequences better than 10.0: 21
length of query: 158
length of database: 5,674,871
effective HSP length: 15
effective length of query: 143
effective length of database: 5,571,296
effective search space: 796695328
effective search space used: 796695328
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 13 (26.3 bits)
dna update 2008.12. 4
Homology vs DNA 
Query= Contig-U12850-1 (Contig-U12850-1Q) /CSM_Contig/Contig-U12850-1Q.Seq.d
         (158 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

(BJ357631) Dictyostelium discoideum cDNA clone:dda64n06, 3' ...   105   4e-19  1
(BJ357674) Dictyostelium discoideum cDNA clone:dda64h07, 3' ...    80   2e-11  1
(BJ351272) Dictyostelium discoideum cDNA clone:dda42k13, 3' ...    74   1e-09  1
(BJ349926) Dictyostelium discoideum cDNA clone:dda38i01, 3' ...    74   1e-09  1
(BJ355452) Dictyostelium discoideum cDNA clone:dda57k03, 3' ...    68   9e-08  1
(BJ353304) Dictyostelium discoideum cDNA clone:dda49n15, 3' ...    68   9e-08  1
(BJ349063) Dictyostelium discoideum cDNA clone:dda35c10, 3' ...    46   0.34   1

>(BJ357631) Dictyostelium discoideum cDNA clone:dda64n06, 3' end,
           single read.
          Length = 149

 Score =  105 bits (53), Expect = 4e-19
 Identities = 134/134 (100%)
 Strand = Plus / Minus


Query: 14  ttaaattcattnnccgntnaaaatnngattgnaaaannttttgaanananaaaatncann 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 146 ttaaattcattnnccgntnaaaatnngattgnaaaannttttgaanananaaaatncann 87


Query: 74  aaagcnnttagatcncttnattantttcgtttaaaaatttgtnnnaaacatgntnttgga 133
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86  aaagcnnttagatcncttnattantttcgtttaaaaatttgtnnnaaacatgntnttgga 27


Query: 134 atcgccnaacntta 147
           ||||||||||||||
Sbjct: 26  atcgccnaacntta 13

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 38,869,445
Number of extensions: 2325813
Number of successful extensions: 312224
Number of sequences better than 10.0: 8
Length of query: 158
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 136
Effective length of database: 93,199,600,587
Effective search space: 12675145679832
Effective search space used: 12675145679832
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 4
Homology vs Protein 
Query= Contig-U12850-1 (Contig-U12850-1Q) /CSM_Contig/Contig-U12850-1Q.Seq.d
         (158 letters)

Database: nrp_B
           3,236,559 sequences; 1,051,180,864 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

FJ374909_1(FJ374909|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374912_2(FJ374912|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374903_1(FJ374903|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374905_1(FJ374905|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374918_1(FJ374918|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374922_1(FJ374922|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374915_1(FJ374915|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374895_1(FJ374895|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374902_1(FJ374902|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374893_1(FJ374893|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374919_1(FJ374919|pid:none) Dictyostelium discoideum strain QS...    37   0.17
FJ374921_1(FJ374921|pid:none) Dictyostelium discoideum strain QS...    36   0.48

>FJ374909_1(FJ374909|pid:none) Dictyostelium discoideum strain QS41
           LagB1 gene, complete cds.
           &FJ374916_1(FJ374916|pid:none)
          Length = 902

 Score = 37.4 bits (85), Expect = 0.17
 Identities = 23/49 (46%), Positives = 24/49 (48%)
 Frame = +2

Query: 11  ALNSXXXXNXIXKXFEXXKXXKAXRSLXXFRLKICXKHXXGIAXXXXFG 157
           AL S    N I K FE  K  KA RSL   RLK+  KH   IA    FG
Sbjct: 820 ALISFAAKNQIEKYFEERKSRKAFRSLDNLRLKLRQKHATEIAKHYTFG 868

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: 46,450,217
Number of extensions: 3966237
Number of successful extensions: 25
Number of sequences better than 10.0: 12
Number of HSP's gapped: 25
Number of HSP's successfully gapped: 12
Length of query: 52
Length of database: 1,051,180,864
Length adjustment: 25
Effective length of query: 27
Effective length of database: 970,266,889
Effective search space: 26197206003
Effective search space used: 26197206003
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: 25 (14.2 bits)
PSORT 

 psg: 0.76  gvh: 0.33  alm: 0.55  top: 0.53  tms: 0.00  mit: 0.26  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  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 

	 44.0 %: cytoplasmic
	 28.0 %: nuclear
	 12.0 %: cytoskeletal
	 12.0 %: mitochondrial
	  4.0 %: peroxisomal

>> prediction for Contig-U12850-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 1
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