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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-U06182-1
Contig ID Contig-U06182-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U06182-1 (Contig-U06182-1Q) /CSM_Contig/Contig-U06182-1Q.Seq.d
CAACACCAACAACAACAAAAACAACAGCAGCACCTGAAAAATCTCATCCA
TCATGGGAAGCAAAGAAAAAAACAAAAAATTTCGACAACAATCCAAATTG
GTAATAAAAATAATGATATAGTTACTTTTGATGATTAATTAATTAAATAA
TAAAAAAAAAAAAAAAAAAAAAAANGAAAAAAAAA
Gap no gap
Contig length 185
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 3210801
End point 3210986
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 2
Link to clone list U06182
List of clone(s) 

est1=VFG704F,1,186
est2=VFG704Z,1,113
Translated Amino Acid sequence 
QHQQQQKQQQHLKNLIHHGKQRKKQKISTTIQIGNKNNDIVTFDD*lik**kkkkkkkxk
k
Translated Amino Acid sequence (All Frames) 
Frame A:
QHQQQQKQQQHLKNLIHHGKQRKKQKISTTIQIGNKNNDIVTFDD*lik**kkkkkkkxk
k


Frame B:
ntnnnknnsst*kissimgskeknkkfrqqsklvikimi*lllmin*lnnkkkkkkkxek
k


Frame C:
tptttkttaapekshpsweakkktknfdnnpnw**k**ysyf**lin*iikkkkkkkxkk
k
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U06182-1 (Contig-U06182-1Q)
/CSM_Contig/Contig-U06182-1Q.Seq.d
         (185 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U06182-1 (Contig-U06182-1Q) /CSM_Contig/Conti...   143  7e-35
Contig-U13650-1 (Contig-U13650-1Q) /CSM_Contig/Conti...    56  1e-08
Contig-U06635-1 (Contig-U06635-1Q) /CSM_Contig/Conti...    52  2e-07
Contig-U11853-1 (Contig-U11853-1Q) /CSM_Contig/Conti...    48  3e-06
Contig-U11147-1 (Contig-U11147-1Q) /CSM_Contig/Conti...    48  3e-06
Contig-U03832-1 (Contig-U03832-1Q) /CSM_Contig/Conti...    48  3e-06
Contig-U13531-1 (Contig-U13531-1Q) /CSM_Contig/Conti...    44  5e-05
Contig-U13114-1 (Contig-U13114-1Q) /CSM_Contig/Conti...    44  5e-05
Contig-U12952-1 (Contig-U12952-1Q) /CSM_Contig/Conti...    44  5e-05
Contig-U13195-1 (Contig-U13195-1Q) /CSM_Contig/Conti...    38  0.003

>Contig-U06182-1 (Contig-U06182-1Q) /CSM_Contig/Contig-U06182-1Q.Seq.d
          Length = 185

 Score =  143 bits (72), Expect = 7e-35
 Identities = 72/72 (100%)
 Strand = Plus / Plus

                                                                       
Query: 80  tttcgacaacaatccaaattggtaataaaaataatgatatagttacttttgatgattaat 139
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 80  tttcgacaacaatccaaattggtaataaaaataatgatatagttacttttgatgattaat 139

                       
Query: 140 taattaaataat 151
           ||||||||||||
Sbjct: 140 taattaaataat 151


 Score =  129 bits (65), Expect = 1e-30
 Identities = 65/65 (100%)
 Strand = Plus / Plus

                                                                      
Query: 1  caacaccaacaacaacaaaaacaacagcagcacctgaaaaatctcatccatcatgggaag 60
          ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  caacaccaacaacaacaaaaacaacagcagcacctgaaaaatctcatccatcatgggaag 60

               
Query: 61 caaag 65
          |||||
Sbjct: 61 caaag 65


>Contig-U13650-1 (Contig-U13650-1Q) /CSM_Contig/Contig-U13650-1Q.Seq.d
          Length = 659

 Score = 56.0 bits (28), Expect = 1e-08
 Identities = 31/32 (96%)
 Strand = Plus / Plus

                                           
Query: 1   caacaccaacaacaacaaaaacaacagcagca 32
           ||||| ||||||||||||||||||||||||||
Sbjct: 164 caacaacaacaacaacaaaaacaacagcagca 195


 Score = 38.2 bits (19), Expect = 0.003
 Identities = 22/23 (95%)
 Strand = Plus / Plus

                                  
Query: 4   caccaacaacaacaaaaacaaca 26
           ||||||||||||||| |||||||
Sbjct: 155 caccaacaacaacaacaacaaca 177


 Score = 32.2 bits (16), Expect = 0.19
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 7   caacaacaacaaaaacaaca 26
           |||||||||||| |||||||
Sbjct: 161 caacaacaacaacaacaaca 180


 Score = 32.2 bits (16), Expect = 0.19
 Identities = 22/24 (91%)
 Strand = Plus / Plus

                                   
Query: 1   caacaccaacaacaacaaaaacaa 24
           ||||| |||||||||||| |||||
Sbjct: 158 caacaacaacaacaacaacaacaa 181


>Contig-U06635-1 (Contig-U06635-1Q) /CSM_Contig/Contig-U06635-1Q.Seq.d
          Length = 325

 Score = 52.0 bits (26), Expect = 2e-07
 Identities = 32/34 (94%)
 Strand = Plus / Plus

                                             
Query: 1   caacaccaacaacaacaaaaacaacagcagcacc 34
           ||||| |||||||||||||||||||| |||||||
Sbjct: 143 caacaacaacaacaacaaaaacaacaacagcacc 176


 Score = 40.1 bits (20), Expect = 8e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 7   caacaacaacaaaaacaaca 26
           ||||||||||||||||||||
Sbjct: 110 caacaacaacaaaaacaaca 129


 Score = 40.1 bits (20), Expect = 8e-04
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                               
Query: 7   caacaacaacaaaaacaaca 26
           ||||||||||||||||||||
Sbjct: 125 caacaacaacaaaaacaaca 144


 Score = 32.2 bits (16), Expect = 0.19
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 7   caacaacaacaaaaacaaca 26
           |||||||||||| |||||||
Sbjct: 140 caacaacaacaacaacaaca 159


 Score = 32.2 bits (16), Expect = 0.19
 Identities = 19/20 (95%)
 Strand = Plus / Plus

                               
Query: 13  caacaaaaacaacagcagca 32
           |||||||||||||| |||||
Sbjct: 89  caacaaaaacaacaacagca 108


 Score = 30.2 bits (15), Expect = 0.75
 Identities = 21/23 (91%)
 Strand = Plus / Plus

                                  
Query: 2   aacaccaacaacaacaaaaacaa 24
           |||| |||||||||||| |||||
Sbjct: 138 aacaacaacaacaacaacaacaa 160


 Score = 30.2 bits (15), Expect = 0.75
 Identities = 18/19 (94%)
 Strand = Plus / Plus

                              
Query: 8   aacaacaacaaaaacaaca 26
           ||||||||||| |||||||
Sbjct: 138 aacaacaacaacaacaaca 156


 Score = 28.2 bits (14), Expect = 3.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 4   caccaacaacaaca 17
           ||||||||||||||
Sbjct: 176 caccaacaacaaca 189


 Score = 28.2 bits (14), Expect = 3.0
 Identities = 17/18 (94%)
 Strand = Plus / Plus

                             
Query: 1   caacaccaacaacaacaa 18
           ||||| ||||||||||||
Sbjct: 101 caacagcaacaacaacaa 118


  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: 12,580
Number of Sequences: 6905
Number of extensions: 12580
Number of successful extensions: 8266
Number of sequences better than 10.0: 1015
length of query: 185
length of database: 5,674,871
effective HSP length: 15
effective length of query: 170
effective length of database: 5,571,296
effective search space: 947120320
effective search space used: 947120320
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. 7
Homology vs DNA 
Query= Contig-U06182-1 (Contig-U06182-1Q) /CSM_Contig/Contig-U06182-1Q.Seq.d
         (185 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

(BJ413071) Dictyostelium discoideum cDNA clone:ddv14h01, 5' ...    78   5e-14  2
(BJ431409) Dictyostelium discoideum cDNA clone:ddv14h01, 3' ...    78   5e-14  2

>(BJ413071) Dictyostelium discoideum cDNA clone:ddv14h01, 5' end,
          single read.
          Length = 186

 Score = 77.8 bits (39), Expect(2) = 5e-14
 Identities = 39/39 (100%)
 Strand = Plus / Plus


Query: 27 gcagcacctgaaaaatctcatccatcatgggaagcaaag 65
          |||||||||||||||||||||||||||||||||||||||
Sbjct: 27 gcagcacctgaaaaatctcatccatcatgggaagcaaag 65

 Score = 30.2 bits (15), Expect(2) = 5e-14
 Identities = 15/15 (100%)
 Strand = Plus / Plus


Query: 80 tttcgacaacaatcc 94
          |||||||||||||||
Sbjct: 80 tttcgacaacaatcc 94

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 49,079,729
Number of extensions: 2713066
Number of successful extensions: 669305
Number of sequences better than 10.0: 2
Length of query: 185
Length of database: 95,242,211,685
Length adjustment: 22
Effective length of query: 163
Effective length of database: 93,199,600,587
Effective search space: 15191534895681
Effective search space used: 15191534895681
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.21
Homology vs Protein 
Query= Contig-U06182-1 (Contig-U06182-1Q) /CSM_Contig/Contig-U06182-1Q.Seq.d
         (185 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: 172,073,615
Number of extensions: 1540103
Number of successful extensions: 4862
Number of sequences better than 10.0: 0
Number of HSP's gapped: 4862
Number of HSP's successfully gapped: 0
Length of query: 61
Length of database: 1,040,966,779
Length adjustment: 33
Effective length of query: 28
Effective length of database: 935,225,374
Effective search space: 26186310472
Effective search space used: 26186310472
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: 0.51  gvh: 0.10  alm: 0.60  top: 0.53  tms: 0.00  mit: 0.29  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 

	 56.0 %: nuclear
	 24.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: mitochondrial
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U06182-1 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