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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-U02566-1
Contig ID Contig-U02566-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U02566-1 (Contig-U02566-1Q) /CSM_Contig/Contig-U02566-1Q.Seq.d
CCACTGCCAACACCAACACCAACACCAACACCACAACCACAGGAACATCA
ACATCAACAAATAATCAATCACCATTTTTAACGAAATTACAGCAACAACA
AAAGGTAAAAG
Gap no gap
Contig length 111
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 7759614
End point 7759725
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U02566
List of clone(s) 

est1=AFE102Z,1,112
Translated Amino Acid sequence 
TANTNTNTNTTTTGTSTSTNNQSPFLTKLQQQQKVK
Translated Amino Acid sequence (All Frames) 
Frame A:
plptptptptpqpqehqhqqiinhhf*rnysnnkr*k


Frame B:
hcqhqhqhqhhnhrninink*sitifneitattkgk


Frame C:
TANTNTNTNTTTTGTSTSTNNQSPFLTKLQQQQKVK
own update 2004. 6. 9
Homology vs CSM-cDNA 
Query= Contig-U02566-1 (Contig-U02566-1Q)
/CSM_Contig/Contig-U02566-1Q.Seq.d
         (111 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U02566-1 (Contig-U02566-1Q) /CSM_Contig/Conti...   101  1e-22
Contig-U11472-1 (Contig-U11472-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U11360-1 (Contig-U11360-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U00886-1 (Contig-U00886-1Q) /CSM_Contig/Conti...    36  0.007
Contig-U12710-1 (Contig-U12710-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U11376-1 (Contig-U11376-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U11235-1 (Contig-U11235-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U09732-1 (Contig-U09732-1Q) /CSM_Contig/Conti...    34  0.028
Contig-U11864-1 (Contig-U11864-1Q) /CSM_Contig/Conti...    32  0.11
Contig-U11683-1 (Contig-U11683-1Q) /CSM_Contig/Conti...    32  0.11

>Contig-U02566-1 (Contig-U02566-1Q) /CSM_Contig/Contig-U02566-1Q.Seq.d
          Length = 111

 Score =  101 bits (51), Expect = 1e-22
 Identities = 51/51 (100%)
 Strand = Plus / Plus

                                                              
Query: 61  ataatcaatcaccatttttaacgaaattacagcaacaacaaaaggtaaaag 111
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  ataatcaatcaccatttttaacgaaattacagcaacaacaaaaggtaaaag 111


>Contig-U11472-1 (Contig-U11472-1Q) /CSM_Contig/Contig-U11472-1Q.Seq.d
          Length = 3643

 Score = 36.2 bits (18), Expect = 0.007
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                  
Query: 89   acagcaacaacaaaaggtaaaa 110
            |||||||||||||||| |||||
Sbjct: 2108 acagcaacaacaaaagataaaa 2129


>Contig-U11360-1 (Contig-U11360-1Q) /CSM_Contig/Contig-U11360-1Q.Seq.d
          Length = 3470

 Score = 36.2 bits (18), Expect = 0.007
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                              
Query: 61   ataatcaatcaccatttt 78
            ||||||||||||||||||
Sbjct: 1529 ataatcaatcaccatttt 1546


  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: 1449
Number of Sequences: 6905
Number of extensions: 1449
Number of successful extensions: 565
Number of sequences better than 10.0: 249
length of query: 111
length of database: 5,674,871
effective HSP length: 14
effective length of query: 97
effective length of database: 5,578,201
effective search space: 541085497
effective search space used: 541085497
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 2009. 5.18
Homology vs DNA 
Query= Contig-U02566-1 (Contig-U02566-1Q) /CSM_Contig/Contig-U02566-1Q.Seq.d
         (111 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

(AC116977) Dictyostelium discoideum chromosome 2 map 5515173...    74   1e-09  1
(BJ341980) Dictyostelium discoideum cDNA clone:dda9c01, 3' e...    74   1e-09  1
(AF506024) Tribolium castaneum isolate pGPUb3 polyubiquitin ...    44   0.94   1
(DT772423) 125606589 TH1 Tribolium castaneum cDNA clone 25M7...    44   0.94   1
(ES553373) TO1010A07pTV TO1 Tribolium castaneum cDNA, mRNA s...    44   0.94   1
(ES545331) TB1006D09pTV TB1 Tribolium castaneum cDNA, mRNA s...    44   0.94   1
(FP017240) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    42   3.7    1
(AC232954) Microcebus murinus clone CH257-205K5, WORKING DRA...    42   3.7    1
(AC199674) Lemur catta clone LB2-211K9, WORKING DRAFT SEQUEN...    42   3.7    1
(AC184727) Microcebus murinus clone CH257-521D18, WORKING DR...    42   3.7    1
(AC171880) Bos taurus clone CH240-279A5, WORKING DRAFT SEQUE...    42   3.7    1
(AC167427) Bos taurus clone CH240-210L2, WORKING DRAFT SEQUE...    42   3.7    1
(CL409733) RPCI44_417B22.r RPCI-44 Sus scrofa genomic clone ...    42   3.7    1
(EG628233) EMBRYOF101125O10 POSSUM_01-POSSUM-C-EMBRYO-2KB Tr...    42   3.7    1
(EG624142) EMBRYOF095453K19 POSSUM_01-POSSUM-C-EMBRYO-2KB Tr...    42   3.7    1
(DY613010) IMMUNEF078647L21 POSSUM_01-C-POSSUM-IMMUNE-2KB Tr...    42   3.7    1
(CR543861) Acinetobacter sp. ADP1 complete genome.                 42   3.7    1

>(AC116977) Dictyostelium discoideum chromosome 2 map 5515173-5817331
              strain AX4, complete sequence.
          Length = 302156

 Score = 73.8 bits (37), Expect = 1e-09
 Identities = 37/37 (100%)
 Strand = Plus / Plus


Query: 75     tttttaacgaaattacagcaacaacaaaaggtaaaag 111
              |||||||||||||||||||||||||||||||||||||
Sbjct: 167178 tttttaacgaaattacagcaacaacaaaaggtaaaag 167214

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 43,087,372
Number of extensions: 3885093
Number of successful extensions: 1038909
Number of sequences better than 10.0: 17
Length of query: 111
Length of database: 101,790,757,118
Length adjustment: 22
Effective length of query: 89
Effective length of database: 99,544,435,898
Effective search space: 8859454794922
Effective search space used: 8859454794922
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)
protein update 2009. 7.19
Homology vs Protein 
Query= Contig-U02566-1 (Contig-U02566-1Q) /CSM_Contig/Contig-U02566-1Q.Seq.d
         (111 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116977_64(AC116977|pid:none) Dictyostelium discoideum chromoso...    33   3.2

>AC116977_64(AC116977|pid:none) Dictyostelium discoideum chromosome
           2 map 5515173-5817331 strain AX4, complete sequence.
          Length = 914

 Score = 33.1 bits (74), Expect = 3.2
 Identities = 15/15 (100%), Positives = 15/15 (100%)
 Frame = +3

Query: 66  QSPFLTKLQQQQKVK 110
           QSPFLTKLQQQQKVK
Sbjct: 479 QSPFLTKLQQQQKVK 493

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: 60,769,656
Number of extensions: 377499
Number of successful extensions: 435
Number of sequences better than 10.0: 1
Number of HSP's gapped: 428
Number of HSP's successfully gapped: 1
Length of query: 37
Length of database: 1,051,180,864
Length adjustment: 11
Effective length of query: 26
Effective length of database: 1,015,578,715
Effective search space: 26405046590
Effective search space used: 26405046590
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: 24 (13.9 bits)
PSORT 

 psg: 0.85  gvh: 0.28  alm: 0.71  top: 0.67  tms: 0.00  mit: 0.50  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 

	 52.0 %: mitochondrial
	 32.0 %: nuclear
	  8.0 %: cytoskeletal
	  8.0 %: cytoplasmic

>> prediction for Contig-U02566-1 is mit
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 1
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