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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-U13326-1
Contig ID Contig-U13326-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13326-1 (Contig-U13326-1Q) /CSM_Contig/Contig-U13326-1Q.Seq.d
AATGACTCAACAAATCTTGGAGAGTATGCAAAATACTTTCCAATCTATGG
ATGGTCCAACCATTAAACGTCTGGCCACAACCATTCAATATGGTTCAAAG
GATGTCGATGAACAACAAATTCATTCAACCCTCGTTAAAGGTGCTGGTGC
TGAATTAAGTTCTCGTGCTCATGAGTGTTTCATTAGTGCCTTGGATATTG
CCTCTGATTATACCTACGAGAAAATTACCATTGGCTTGGA
Gap no gap
Contig length 240
Chromosome number (1..6, M) 6
Chromosome length 3595308
Start point 1728259
End point 1728019
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U13326
List of clone(s) 

est1=SLD154F,1,241
Translated Amino Acid sequence 
MTQQILESMQNTFQSMDGPTIKRLATTIQYGSKDVDEQQIHSTLVKGAGAELSSRAHECF
ISALDIASDYTYEKITIGL
Translated Amino Acid sequence (All Frames) 
Frame A:
ndstnlgeyakyfpiygwsnh*tsghnhsiwfkgcr*ttnsfnpr*rcwc*ikfscs*vf
h*clgycl*lylrenyhwlg


Frame B:
MTQQILESMQNTFQSMDGPTIKRLATTIQYGSKDVDEQQIHSTLVKGAGAELSSRAHECF
ISALDIASDYTYEKITIGL


Frame C:
*lnkswrvckilsnlwmvqplnvwpqpfnmvqrmsmnnkfiqpslkvlvln*vlvlmsvs
lvpwilpliiptrklplaw
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13326-1 (Contig-U13326-1Q)
/CSM_Contig/Contig-U13326-1Q.Seq.d
         (240 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13326-1 (Contig-U13326-1Q) /CSM_Contig/Conti...   476  e-135
Contig-U11404-1 (Contig-U11404-1Q) /CSM_Contig/Conti...    56  2e-08
Contig-U11269-1 (Contig-U11269-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U10681-1 (Contig-U10681-1Q) /CSM_Contig/Conti...    32  0.25
Contig-U14313-1 (Contig-U14313-1Q) /CSM_Contig/Conti...    30  1.00
Contig-U12907-1 (Contig-U12907-1Q) /CSM_Contig/Conti...    30  1.00
Contig-U12802-1 (Contig-U12802-1Q) /CSM_Contig/Conti...    30  1.00
Contig-U12181-1 (Contig-U12181-1Q) /CSM_Contig/Conti...    30  1.00
Contig-U09144-1 (Contig-U09144-1Q) /CSM_Contig/Conti...    30  1.00

>Contig-U13326-1 (Contig-U13326-1Q) /CSM_Contig/Contig-U13326-1Q.Seq.d
          Length = 240

 Score =  476 bits (240), Expect = e-135
 Identities = 240/240 (100%)
 Strand = Plus / Plus

                                                                       
Query: 1   aatgactcaacaaatcttggagagtatgcaaaatactttccaatctatggatggtccaac 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   aatgactcaacaaatcttggagagtatgcaaaatactttccaatctatggatggtccaac 60

                                                                       
Query: 61  cattaaacgtctggccacaaccattcaatatggttcaaaggatgtcgatgaacaacaaat 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  cattaaacgtctggccacaaccattcaatatggttcaaaggatgtcgatgaacaacaaat 120

                                                                       
Query: 121 tcattcaaccctcgttaaaggtgctggtgctgaattaagttctcgtgctcatgagtgttt 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 tcattcaaccctcgttaaaggtgctggtgctgaattaagttctcgtgctcatgagtgttt 180

                                                                       
Query: 181 cattagtgccttggatattgcctctgattatacctacgagaaaattaccattggcttgga 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 cattagtgccttggatattgcctctgattatacctacgagaaaattaccattggcttgga 240


>Contig-U11404-1 (Contig-U11404-1Q) /CSM_Contig/Contig-U11404-1Q.Seq.d
          Length = 1628

 Score = 56.0 bits (28), Expect = 2e-08
 Identities = 28/28 (100%)
 Strand = Plus / Plus

                                       
Query: 213 cctacgagaaaattaccattggcttgga 240
           ||||||||||||||||||||||||||||
Sbjct: 921 cctacgagaaaattaccattggcttgga 948


>Contig-U11269-1 (Contig-U11269-1Q) /CSM_Contig/Contig-U11269-1Q.Seq.d
          Length = 2060

 Score = 32.2 bits (16), Expect = 0.25
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                            
Query: 191  ttggatattgcctctg 206
            ||||||||||||||||
Sbjct: 1811 ttggatattgcctctg 1826


  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: 1596
Number of Sequences: 6905
Number of extensions: 1596
Number of successful extensions: 522
Number of sequences better than 10.0: 45
length of query: 240
length of database: 5,674,871
effective HSP length: 15
effective length of query: 225
effective length of database: 5,571,296
effective search space: 1253541600
effective search space used: 1253541600
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 2008.12. 7
Homology vs DNA 
Query= Contig-U13326-1 (Contig-U13326-1Q) /CSM_Contig/Contig-U13326-1Q.Seq.d
         (240 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

(AF388524) Dictyostelium discoideum carmil gene, complete cds.    476   e-130  1
(AU061096) Dictyostelium discoideum slug cDNA, clone SLD154.      476   e-130  1
(BJ445102) Dictyostelium discoideum cDNA clone:ddv58o08, 3' ...    56   6e-04  1
(BJ443756) Dictyostelium discoideum cDNA clone:ddv54d02, 3' ...    54   0.002  1
(BV007035) sa09h10.x1 Gm-p1 Glycine max STS genomic, sequenc...    44   2.1    1
(AL732391) Mouse DNA sequence from clone RP23-364H13 on chro...    44   2.1    1
(AC146896) Mus musculus chromosome X clone xcat-28-97f16, co...    44   2.1    1
(AC093447) Mus musculus strain 129/Sv clone ct7-25g12 map X,...    44   2.1    1
(AZ044923) B164/F Soybean genomic clone Glycine max genomic ...    44   2.1    1
(AQ842169) T134462 Soybean RFLP probe Glycine max genomic cl...    44   2.1    1
(EJ798030) 1093017411218 Global-Ocean-Sampling_GS-30-02-01-1...    44   2.1    1
(EJ765412) 1092963204337 Global-Ocean-Sampling_GS-30-02-01-1...    44   2.1    1
(EJ764040) 1092963168593 Global-Ocean-Sampling_GS-30-02-01-1...    44   2.1    1
(EJ546810) 1092957880381 Global-Ocean-Sampling_GS-29-01-01-1...    44   2.1    1
(EJ524105) 1092955170085 Global-Ocean-Sampling_GS-29-01-01-1...    44   2.1    1
(AC212229) Zea mays chromosome 2 clone CH201-30I1; ZMMBBc003...    42   8.4    1
(AC191065) Zea mays chromosome 2 clone CH201-117O22; ZMMBBc0...    42   8.4    1
(ER391028) 1095328006081 Global-Ocean-Sampling_GS-34-01-01-1...    42   8.4    1
(EJ218981) 1092351176262 Global-Ocean-Sampling_GS-27-01-01-1...    42   8.4    1
(DT969956) CLJ125-F09.y1d-s SHGC-CLJ Gasterosteus aculeatus ...    42   8.4    1
(DT954391) CFW133-A02.y1d-s SHGC-CFW Gasterosteus aculeatus ...    42   8.4    1
(DT954376) CFW132-H04.y1d-s SHGC-CFW Gasterosteus aculeatus ...    42   8.4    1
(DT951625) CFW116-D06.y1d-s SHGC-CFW Gasterosteus aculeatus ...    42   8.4    1
(DN674558) CFW81-B03.y1d-s SHGC-CFW Gasterosteus aculeatus c...    42   8.4    1
(CD508697) CDA92-C08.x1d-t SHGC-CDA Gasterosteus aculeatus c...    42   8.4    1
(CD499540) CDA39-H08.x1d-t SHGC-CDA Gasterosteus aculeatus c...    42   8.4    1

>(AF388524) Dictyostelium discoideum carmil gene, complete cds.
          Length = 3780

 Score =  476 bits (240), Expect = e-130
 Identities = 240/240 (100%)
 Strand = Plus / Plus


Query: 1    aatgactcaacaaatcttggagagtatgcaaaatactttccaatctatggatggtccaac 60
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2774 aatgactcaacaaatcttggagagtatgcaaaatactttccaatctatggatggtccaac 2833


Query: 61   cattaaacgtctggccacaaccattcaatatggttcaaaggatgtcgatgaacaacaaat 120
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2834 cattaaacgtctggccacaaccattcaatatggttcaaaggatgtcgatgaacaacaaat 2893


Query: 121  tcattcaaccctcgttaaaggtgctggtgctgaattaagttctcgtgctcatgagtgttt 180
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2894 tcattcaaccctcgttaaaggtgctggtgctgaattaagttctcgtgctcatgagtgttt 2953


Query: 181  cattagtgccttggatattgcctctgattatacctacgagaaaattaccattggcttgga 240
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2954 cattagtgccttggatattgcctctgattatacctacgagaaaattaccattggcttgga 3013

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 224,096,209
Number of extensions: 11241701
Number of successful extensions: 2956623
Number of sequences better than 10.0: 26
Length of query: 240
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 217
Effective length of database: 93,106,754,628
Effective search space: 20204165754276
Effective search space used: 20204165754276
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13326-1 (Contig-U13326-1Q) /CSM_Contig/Contig-U13326-1Q.Seq.d
         (240 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AF388524_1(AF388524|pid:none) Dictyostelium discoideum carmil ge...   157   1e-37
AF006034_3(AF006034|pid:none) Clostridium pasteurianum 1,3-propa...    32   6.9

>AF388524_1(AF388524|pid:none) Dictyostelium discoideum carmil gene,
           complete cds.
          Length = 1050

 Score =  157 bits (396), Expect = 1e-37
 Identities = 79/79 (100%), Positives = 79/79 (100%)
 Frame = +2

Query: 2   MTQQILESMQNTFQSMDGPTIKRLATTIQYGSKDVDEQQIHSTLVKGAGAELSSRAHECF 181
           MTQQILESMQNTFQSMDGPTIKRLATTIQYGSKDVDEQQIHSTLVKGAGAELSSRAHECF
Sbjct: 759 MTQQILESMQNTFQSMDGPTIKRLATTIQYGSKDVDEQQIHSTLVKGAGAELSSRAHECF 818

Query: 182 ISALDIASDYTYEKITIGL 238
           ISALDIASDYTYEKITIGL
Sbjct: 819 ISALDIASDYTYEKITIGL 837

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: 463,319,160
Number of extensions: 9802644
Number of successful extensions: 16385
Number of sequences better than 10.0: 2
Number of HSP's gapped: 16323
Number of HSP's successfully gapped: 2
Length of query: 80
Length of database: 1,051,180,864
Length adjustment: 51
Effective length of query: 29
Effective length of database: 886,116,355
Effective search space: 25697374295
Effective search space used: 25697374295
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: 27 (15.0 bits)
PSORT 

 psg: 0.75  gvh: 0.49  alm: 0.52  top: 0.53  tms: 0.00  mit: 0.28  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 %: cytoplasmic
	 32.0 %: nuclear
	 16.0 %: mitochondrial
	 12.0 %: cytoskeletal
	  4.0 %: vacuolar
	  4.0 %: endoplasmic reticulum

>> prediction for Contig-U13326-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 1
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