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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U06586-1
Contig ID Contig-U06586-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06586-1 (Contig-U06586-1Q) /CSM_Contig/Contig-U06586-1Q.Seq.d
GAAAAAAAGTAGTGTAAAAATTAAATAAATAAACAAATTAATTAATTAAT
ATTTTTTAAAATTAAAATCCAAAATCTTTTTTTGTTATTTTAATATCACT
ATTAATAAATTTTGATTTTCCAAAATTTAATTTTTTTTTTTTCAAAATTT
TCTTTTTTTANACTGCNCCCTTTCAAGTTCACACACTCCCTACATTTTTT
TTAAATTAAAAATTATATTTATTTTTTAAATTTTTATTTTTTCATTATTT
AATTTCTTTTTTTTTTTTAATACACGATATTTTNATTTTTTTTCATAATA
ATATCAAATTAAATCNGNAATAAACTTTTTNTAAATAAAATAAAAAAAAA
ANNNNNNNNNNCCCTTTCAAGTTCACACACTCCCTACATTTTTTTTAAAT
Gap no gap
Contig length 400
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 6706112
End point 6706465
Strand (PLUS/MINUS) PLUS
Number of clones 4
Number of EST 4
Link to clone list U06586
List of clone(s) 

est1=VSI303F,1,273
est2=VSJ504F,1,271
est3=VSD686E,182,401
est4=VSF686F,182,351
Translated Amino Acid sequence 
kkvv*klnk*tn*linif*n*NPKSFFVILISLLINFDFPKFNFFFFKIFFFXTAPFQVH
TLPTFFLN*klylffkflffhylisffflihdixiffhnniklnxx*tfxk*nkkkxxxx
pfkfthslhff*
Translated Amino Acid sequence (All Frames) 
Frame A:
ekk*ckn*inkqin*liffkikiqnlfllf*yhy**ilifqnlifffskfsffxlxpfkf
thslhff*iknyiyflnfyffii*flfff*ytifxfffiiisn*ixnklfxnkikkkxxx
xlssshtpyiffk


Frame B:
kkssvkik*inklin*yflklkskiffcyfnitinkf*fski*ffffqnflflxcxlsss
htpyiffklkiifif*ififslfnfffffntryfxffs**yqiksxinfx*ik*kkxxxx
pfqvhtlptffln


Frame C:
kkvv*klnk*tn*linif*n*NPKSFFVILISLLINFDFPKFNFFFFKIFFFXTAPFQVH
TLPTFFLN*klylffkflffhylisffflihdixiffhnniklnxx*tfxk*nkkkxxxx
pfkfthslhff*
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06586-1 (Contig-U06586-1Q)
/CSM_Contig/Contig-U06586-1Q.Seq.d
         (400 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06586-1 (Contig-U06586-1Q) /CSM_Contig/Conti...    94  1e-19
Contig-U10367-1 (Contig-U10367-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U09236-1 (Contig-U09236-1Q) /CSM_Contig/Conti...    38  0.007
Contig-U11174-1 (Contig-U11174-1Q) /CSM_Contig/Conti...    34  0.11
Contig-U14446-1 (Contig-U14446-1Q) /CSM_Contig/Conti...    32  0.43
Contig-U13243-1 (Contig-U13243-1Q) /CSM_Contig/Conti...    32  0.43
Contig-U09699-1 (Contig-U09699-1Q) /CSM_Contig/Conti...    32  0.43
Contig-U09437-1 (Contig-U09437-1Q) /CSM_Contig/Conti...    32  0.43
Contig-U07980-1 (Contig-U07980-1Q) /CSM_Contig/Conti...    32  0.43

>Contig-U06586-1 (Contig-U06586-1Q) /CSM_Contig/Contig-U06586-1Q.Seq.d
          Length = 400

 Score = 93.7 bits (47), Expect = 1e-19
 Identities = 47/47 (100%)
 Strand = Plus / Plus

                                                          
Query: 84  gttattttaatatcactattaataaattttgattttccaaaatttaa 130
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 84  gttattttaatatcactattaataaattttgattttccaaaatttaa 130


 Score = 77.8 bits (39), Expect = 8e-15
 Identities = 48/48 (100%)
 Strand = Plus / Plus

                                                           
Query: 294 cataataatatcaaattaaatcngnaataaactttttntaaataaaat 341
           ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 294 cataataatatcaaattaaatcngnaataaactttttntaaataaaat 341


 Score = 58.0 bits (29), Expect = 8e-09
 Identities = 32/32 (100%)
 Strand = Plus / Plus

                                           
Query: 162 actgcnccctttcaagttcacacactccctac 193
           ||||||||||||||||||||||||||||||||
Sbjct: 162 actgcnccctttcaagttcacacactccctac 193


 Score = 54.0 bits (27), Expect = 1e-07
 Identities = 27/27 (100%)
 Strand = Plus / Plus

                                      
Query: 362 ccctttcaagttcacacactccctaca 388
           |||||||||||||||||||||||||||
Sbjct: 168 ccctttcaagttcacacactccctaca 194


 Score = 54.0 bits (27), Expect = 1e-07
 Identities = 27/27 (100%)
 Strand = Plus / Plus

                                      
Query: 362 ccctttcaagttcacacactccctaca 388
           |||||||||||||||||||||||||||
Sbjct: 362 ccctttcaagttcacacactccctaca 388


 Score = 52.0 bits (26), Expect = 5e-07
 Identities = 26/26 (100%)
 Strand = Plus / Plus

                                     
Query: 168 ccctttcaagttcacacactccctac 193
           ||||||||||||||||||||||||||
Sbjct: 362 ccctttcaagttcacacactccctac 387


>Contig-U10367-1 (Contig-U10367-1Q) /CSM_Contig/Contig-U10367-1Q.Seq.d
          Length = 1187

 Score = 40.1 bits (20), Expect = 0.002
 Identities = 23/24 (95%)
 Strand = Plus / Plus

                                    
Query: 107  aaattttgattttccaaaatttaa 130
            |||||| |||||||||||||||||
Sbjct: 1067 aaatttcgattttccaaaatttaa 1090


 Score = 28.2 bits (14), Expect = 6.7
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                          
Query: 106  taaattttgatttt 119
            ||||||||||||||
Sbjct: 1110 taaattttgatttt 1097


>Contig-U09236-1 (Contig-U09236-1Q) /CSM_Contig/Contig-U09236-1Q.Seq.d
          Length = 507

 Score = 38.2 bits (19), Expect = 0.007
 Identities = 22/23 (95%)
 Strand = Plus / Minus

                                  
Query: 86  tattttaatatcactattaataa 108
           ||||||||||||||| |||||||
Sbjct: 504 tattttaatatcacttttaataa 482


  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: 2571
Number of Sequences: 6905
Number of extensions: 2571
Number of successful extensions: 304
Number of sequences better than 10.0: 92
length of query: 400
length of database: 5,674,871
effective HSP length: 16
effective length of query: 384
effective length of database: 5,564,391
effective search space: 2136726144
effective search space used: 2136726144
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. 9
Homology vs DNA 
Query= Contig-U06586-1 (Contig-U06586-1Q) /CSM_Contig/Contig-U06586-1Q.Seq.d
         (400 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

(AC115592) Dictyostelium discoideum chromosome 2 map 1-12595...    78   3e-18  2
(AU265620) Dictyostelium discoideum vegetative cDNA clone:VS...    78   3e-10  1
(AU270021) Dictyostelium discoideum vegetative cDNA clone:VS...    58   2e-04  1
(AU268474) Dictyostelium discoideum vegetative cDNA clone:VS...    58   2e-04  1

>(AC115592) Dictyostelium discoideum chromosome 2 map 1-125959 strain
             AX4, complete sequence.
          Length = 125958

 Score = 77.8 bits (39), Expect(2) = 3e-18
 Identities = 45/48 (93%)
 Strand = Plus / Plus


Query: 294   cataataatatcaaattaaatcngnaataaactttttntaaataaaat 341
             |||||||||||||||||||||| | |||||||||||| ||||||||||
Sbjct: 85779 cataataatatcaaattaaatctgtaataaactttttataaataaaat 85826

 Score = 58.0 bits (29), Expect(2) = 3e-18
 Identities = 31/32 (96%)
 Strand = Plus / Plus


Query: 162   actgcnccctttcaagttcacacactccctac 193
             ||||| ||||||||||||||||||||||||||
Sbjct: 85647 actgcaccctttcaagttcacacactccctac 85678

 Score = 54.0 bits (27), Expect = 0.004
 Identities = 27/27 (100%)
 Strand = Plus / Plus


Query: 362   ccctttcaagttcacacactccctaca 388
             |||||||||||||||||||||||||||
Sbjct: 85653 ccctttcaagttcacacactccctaca 85679

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 102,306,689
Number of extensions: 5441600
Number of successful extensions: 323478
Number of sequences better than 10.0: 4
Length of query: 400
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 377
Effective length of database: 93,106,754,628
Effective search space: 35101246494756
Effective search space used: 35101246494756
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.22
Homology vs Protein 
Query= Contig-U06586-1 (Contig-U06586-1Q) /CSM_Contig/Contig-U06586-1Q.Seq.d
         (400 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: 183,847,238
Number of extensions: 1623882
Number of successful extensions: 390
Number of sequences better than 10.0: 0
Number of HSP's gapped: 390
Number of HSP's successfully gapped: 0
Length of query: 133
Length of database: 1,040,966,779
Length adjustment: 98
Effective length of query: 35
Effective length of database: 726,946,849
Effective search space: 25443139715
Effective search space used: 25443139715
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: 29 (15.8 bits)
PSORT 

 psg: 0.99  gvh: 0.62  alm: 0.33  top: 0.47  tms: 0.00  mit: 0.27  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 

	 32.0 %: extracellular, including cell wall
	 24.0 %: cytoplasmic
	 24.0 %: nuclear
	 12.0 %: mitochondrial
	  4.0 %: vacuolar
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U06586-1 is exc
VS (DIR, S) 4
VH (FL, L) 0
VF (FL, S) 0
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