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Dicty_cDB
Contig List | Clone List | cDNA Library List
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NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U05667-1
Contig ID Contig-U05667-1
Contig update 2001. 8.30
Contig sequence 
>Contig-U05667-1 (Contig-U05667-1Q) /CSM_Contig/Contig-U05667-1Q.Seq.d
AAACAAATTACTAAATATACAAAAAAAAAAAAAAAAAAAATGACAATTTT
AGGATCCATAAGCACATTTTCACAATTTAATGTAAAGAAAAGTAAAAGTA
AAAATGATTCAATTACATTATTTCTAAAATCAAATGTTGTTGGGTATACA
AATTCAATGGTTAGCCAAATAGATGGTAGATTCGATAATATTCCACAAAT
TTCTCAAAAACCACCAAATAAACCAAATGCTTACATTTAATCAAGAAAAC
AAGATTTTATTTTGAATTTAAAAATAAAATTATTTCTTTAAGTTTTCTTT
TTGTTCATCAAATTTATTTTAATAAAATATTTTATTTTAAAATCCATTTT
TATTGCTTACAATTAAAAATAAAAAATATATAAAGAGATAAAATAGAAAT
AAAAAAAACTAATAAATAAAAGAAAAAAAAAAAA
Gap no gap
Contig length 434
Chromosome number (1..6, M) 2
Chromosome length 8467578
Start point 1249924
End point 1250359
Strand (PLUS/MINUS) PLUS
Number of clones 3
Number of EST 3
Link to clone list U05667
List of clone(s) 

est1=SSM884E,1,431
est2=SSK332E,18,249
est3=SSL412E,42,435
Translated Amino Acid sequence 
KQITKYTKKKKKKMTILGSISTFSQFNVKKSKSKNDSITLFLKSNVVGYTNSMVSQIDGR
FDNIPQISQKPPNKPNAYI*srkqdfilnlkiklfl*vfflfikfilikyfilksifiay
n*k*kiykeik*k*kklinkrkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
KQITKYTKKKKKKMTILGSISTFSQFNVKKSKSKNDSITLFLKSNVVGYTNSMVSQIDGR
FDNIPQISQKPPNKPNAYI*srkqdfilnlkiklfl*vfflfikfilikyfilksifiay
n*k*kiykeik*k*kklinkrkkk


Frame B:
nkllniqkkkkkk*qf*dp*ahfhnlm*rkvkvkmiqlhyf*nqmllgiqiqwlak*mvd
siifhkflknhqinqmltfnqenkilf*i*k*nyffkfsfcssnlf**nilf*npflllt
iknkkyikr*nrnkkn**ikekkk


Frame C:
tny*iykkkkkkndnfrihkhifti*ckek*k*k*fnyiiskikccwvykfng*pnrw*i
r*ystnfskttk*tkclhlikktrfyfefknkiislsflfvhqiyfnkifyfkihfyclq
lkikni*rdkieikktnk*kkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U05667-1 (Contig-U05667-1Q)
/CSM_Contig/Contig-U05667-1Q.Seq.d
         (434 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U05667-1 (Contig-U05667-1Q) /CSM_Contig/Conti...   444  e-125
Contig-U11806-1 (Contig-U11806-1Q) /CSM_Contig/Conti...    42  5e-04
Contig-U12565-1 (Contig-U12565-1Q) /CSM_Contig/Conti...    40  0.002
Contig-U10806-1 (Contig-U10806-1Q) /CSM_Contig/Conti...    36  0.030
Contig-U09243-1 (Contig-U09243-1Q) /CSM_Contig/Conti...    36  0.030
Contig-U13224-1 (Contig-U13224-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U10972-1 (Contig-U10972-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U04959-1 (Contig-U04959-1Q) /CSM_Contig/Conti...    34  0.12
Contig-U14807-1 (Contig-U14807-1Q) /CSM_Contig/Conti...    32  0.47
Contig-U14298-1 (Contig-U14298-1Q) /CSM_Contig/Conti...    28  7.3

>Contig-U05667-1 (Contig-U05667-1Q) /CSM_Contig/Contig-U05667-1Q.Seq.d
          Length = 434

 Score =  444 bits (224), Expect = e-125
 Identities = 224/224 (100%)
 Strand = Plus / Plus

                                                                       
Query: 41  tgacaattttaggatccataagcacattttcacaatttaatgtaaagaaaagtaaaagta 100
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 41  tgacaattttaggatccataagcacattttcacaatttaatgtaaagaaaagtaaaagta 100

                                                                       
Query: 101 aaaatgattcaattacattatttctaaaatcaaatgttgttgggtatacaaattcaatgg 160
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 101 aaaatgattcaattacattatttctaaaatcaaatgttgttgggtatacaaattcaatgg 160

                                                                       
Query: 161 ttagccaaatagatggtagattcgataatattccacaaatttctcaaaaaccaccaaata 220
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 161 ttagccaaatagatggtagattcgataatattccacaaatttctcaaaaaccaccaaata 220

                                                       
Query: 221 aaccaaatgcttacatttaatcaagaaaacaagattttattttg 264
           ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 221 aaccaaatgcttacatttaatcaagaaaacaagattttattttg 264


 Score = 40.1 bits (20), Expect = 0.002
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                              
Query: 1  aaacaaattactaaatatac 20
          ||||||||||||||||||||
Sbjct: 1  aaacaaattactaaatatac 20


>Contig-U11806-1 (Contig-U11806-1Q) /CSM_Contig/Contig-U11806-1Q.Seq.d
          Length = 1162

 Score = 42.1 bits (21), Expect = 5e-04
 Identities = 21/21 (100%)
 Strand = Plus / Plus

                                
Query: 88  aaaagtaaaagtaaaaatgat 108
           |||||||||||||||||||||
Sbjct: 525 aaaagtaaaagtaaaaatgat 545


>Contig-U12565-1 (Contig-U12565-1Q) /CSM_Contig/Contig-U12565-1Q.Seq.d
          Length = 2077

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

                                    
Query: 209  aaccaccaaataaaccaaatgctt 232
            |||||||||||| |||||||||||
Sbjct: 1570 aaccaccaaatacaccaaatgctt 1547


  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: 4128
Number of Sequences: 6905
Number of extensions: 4128
Number of successful extensions: 430
Number of sequences better than 10.0: 142
length of query: 434
length of database: 5,674,871
effective HSP length: 16
effective length of query: 418
effective length of database: 5,564,391
effective search space: 2325915438
effective search space used: 2325915438
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. 6
Homology vs DNA 
Query= Contig-U05667-1 (Contig-U05667-1Q) /CSM_Contig/Contig-U05667-1Q.Seq.d
         (434 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

(C91480) Dictyostelium discoideum slug cDNA, clone SSK332.        343   3e-90  1
(AC116982) Dictyostelium discoideum chromosome 2 map 3622643...   329   5e-86  1
(C93258) Dictyostelium discoideum slug cDNA, clone SSM884.        113   1e-69  4
(AU074636) Dictyostelium discoideum slug cDNA, clone SSL412.      111   2e-62  3
(AC116920) Dictyostelium discoideum chromosome 2 map 4415041...    98   3e-57  3
(AU038733) Dictyostelium discoideum slug cDNA, clone SSL412.       98   5e-23  2
(CZ546714) SRAA-aad69f04.b1 Strongyloides ratti whole genome...    54   0.004  1
(AC166303) Bos taurus clone CH240-173O1, WORKING DRAFT SEQUE...    34   0.15   2
(AC218409) Bos taurus clone CH240-283M12, WORKING DRAFT SEQU...    34   0.15   2
(CZ542488) SRAA-aad44d10.g1 Strongyloides ratti whole genome...    48   0.26   1
(AP004965) Lotus japonicus genomic DNA, chromosome 1, clone:...    38   0.53   2
(AC117171) Rattus norvegicus clone CH230-25H22, WORKING DRAF...    34   0.55   2
(BB973210) Plasmodium berghei strain ANKA cDNA clone:OK00298...    36   1.0    2
(BX469902) Zebrafish DNA sequence from clone CH211-277G23 in...    46   1.0    1
(AC167976) Mus musculus BAC clone RP23-167L5 from chromosome...    46   1.0    1
(CU571019) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   1.0    1
(DH341276) Oryzias latipes Fosmid clone:GOLWFno711_f23, forw...    46   1.0    1
(DE253486) Oryzias latipes DNA, clone: ola1-122F23.R, genomi...    46   1.0    1
(FG226117) Aats03387 Antheraea assama fifth instar larval te...    46   1.0    1
(FF323427) 280419973 Pea aphid whole body normalized full le...    46   1.0    1
(FF316717) 280377365 Pea aphid whole body normalized full le...    46   1.0    1
(FF303798) 279355463 Pea aphid whole body normalized full le...    46   1.0    1
(EX633781) 256591448 Pea aphid whole body normalized full le...    46   1.0    1
(EX624555) 255426923 Pea aphid whole body normalized full le...    46   1.0    1
(AC116979) Dictyostelium discoideum chromosome 2 map 6445720...    40   1.7    3
(DV789468) Hw_liver_41_050728_A05 Bos taurus CF-24-HW liver ...    38   2.4    2
(ED863895) OA_CBa0010M06.f OA_CBa Oryza australiensis genomi...    32   2.7    2
(EU835853) Cicer arietinum voucher ICCV 10 chloroplast, comp...    34   3.2    5
(BX784031) Zebrafish DNA sequence from clone DKEY-174E15 in ...    44   4.0    1
(AM485409) Vitis vinifera contig VV78X054646.1, whole genome...    44   4.0    1
(AB012243) Arabidopsis thaliana genomic DNA, chromosome 5, P...    44   4.0    1
(EU153401) Felis catus FLA extended class II, class II, clas...    44   4.0    1
(AL591051) Human DNA sequence from clone RP11-613I8 on chrom...    44   4.0    1
(AL138920) Human DNA sequence from clone RP11-148B2 on chrom...    44   4.0    1
(AK090947) Homo sapiens cDNA FLJ33628 fis, clone BRAMY2022445.     44   4.0    1
(AB209698) Homo sapiens mRNA for RAB18, member RAS oncogene ...    44   4.0    1
(AC133221) Rattus norvegicus clone CH230-2A4, *** SEQUENCING...    44   4.0    1
(AL591111) Human DNA sequence *** SEQUENCING IN PROGRESS ***...    44   4.0    1
(AL445484) Human DNA sequence *** SEQUENCING IN PROGRESS ***...    44   4.0    1
(AC184580) Strongylocentrotus purpuratus clone R3-3056O7, WO...    44   4.0    1
(AC181050) Strongylocentrotus purpuratus clone R3-3050K5, WO...    44   4.0    1
(AC178587) Strongylocentrotus purpuratus clone R3-3025C12, W...    44   4.0    1
(AC020586) Homo sapiens chromosome UL clone RP11-93E13, WORK...    44   4.0    1
(AQ382453) RPCI11-167C24.TV RPCI-11 Homo sapiens genomic clo...    44   4.0    1
(ER852737) PPTDO47TF Solanum tuberosum RHPOTKEY BAC ends Sol...    44   4.0    1
(EK310308) 1095462394845 Global-Ocean-Sampling_GS-31-01-01-1...    44   4.0    1
(EJ015609) 1095433016250 Global-Ocean-Sampling_GS-26-01-01-1...    44   4.0    1
(EI891206) CAH1-58B12TR CAA1Ba Cicer arietinum genomic clone...    44   4.0    1
(AL054712) Drosophila melanogaster genome survey sequence T7...    44   4.0    1
(CW335128) 104_833_11482873_116_36074_001 Sorghum methylatio...    44   4.0    1
(CE573123) tigr-gss-dog-17000327528366 Dog Library Canis lup...    44   4.0    1
(AV754832) Homo sapiens cDNA clone:TPAAGF02, 5'end, expresse...    44   4.0    1
(AV754642) Homo sapiens cDNA clone:TPAAGC11, 5'end, expresse...    44   4.0    1
(AV754596) Homo sapiens cDNA clone:TPAAFF09, 5'end, expresse...    44   4.0    1
(CF879064) tric019xm14.b11 T.reesei mycelial culture, Versio...    44   4.0    1
(CF869573) tric019xm14.b1 T.reesei mycelial culture, Version...    44   4.0    1
(CF866499) tric006xo04.b1 T.reesei mycelial culture, Version...    44   4.0    1
(CB899719) tric019xm14 T.reesei mycelial culture, Version 3 ...    44   4.0    1
(CB896475) tric006xo04 T.reesei mycelial culture, Version 3 ...    44   4.0    1
(BX105414) RZPD Homo sapiens cDNA clone IMAGp998C20257 = IMA...    44   4.0    1
(BM668549) UI-E-CK1-afm-e-21-0-UI.s2 UI-E-CK1 Homo sapiens c...    44   4.0    1
(H21669) yl33f10.r1 Soares breast 3NbHBst Homo sapiens cDNA ...    44   4.0    1
(FE919319) AUBB-aaa23e08.g2 A.suum_EST_96hr_Embryo Ascaris s...    44   4.0    1
(AC004676) Homo sapiens chromosome X clone bWXD171, *** SEQU...    42   4.2    2
(AC129147) Rattus norvegicus clone CH230-333G11, WORKING DRA...    40   4.4    2
(AL391397) Human chromosome 14 DNA sequence BAC R-625F13 of ...    36   4.9    4
(AC208197) Zea mays chromosome 4 clone CH201-106A9; ZMMBBc01...    34   5.3    3
(AM443109) Vitis vinifera contig VV78X071910.2, whole genome...    40   5.5    2
(D10997) 'Chlorella' ellipsoidea rbcL, rps14, rps4, atpE, at...    34   7.2    3
(BX640405) Zebrafish DNA sequence *** SEQUENCING CANCELLED *...    30   7.3    2
(BX470117) Zebrafish DNA sequence from clone CH211-204N10 in...    30   7.4    2
(CU928768) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    40   8.6    2
(DU042137) 157727 Tomato HindIII BAC Library Solanum lycoper...    30   10.0   2

>(C91480) Dictyostelium discoideum slug cDNA, clone SSK332.
          Length = 232

 Score =  343 bits (173), Expect = 3e-90
 Identities = 182/185 (98%)
 Strand = Plus / Plus


Query: 41  tgacaattttaggatccataagcacattttcacaatttaatgtaaagaaaagtaaaagta 100
           |||||||||||||||| || ||| ||||||||||||||||||||||||||||||||||||
Sbjct: 24  tgacaattttaggatcaatcagctcattttcacaatttaatgtaaagaaaagtaaaagta 83


Query: 101 aaaatgattcaattacattatttctaaaatcaaatgttgttgggtatacaaattcaatgg 160
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 84  aaaatgattcaattacattatttctaaaatcaaatgttgttgggtatacaaattcaatgg 143


Query: 161 ttagccaaatagatggtagattcgataatattccacaaatttctcaaaaaccaccaaata 220
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 144 ttagccaaatagatggtagattcgataatattccacaaatttctcaaaaaccaccaaata 203


Query: 221 aacca 225
           |||||
Sbjct: 204 aacca 208

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 327,669,919
Number of extensions: 20685483
Number of successful extensions: 1906598
Number of sequences better than 10.0: 74
Length of query: 434
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 411
Effective length of database: 93,106,754,628
Effective search space: 38266876152108
Effective search space used: 38266876152108
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.20
Homology vs Protein 
Query= Contig-U05667-1 (Contig-U05667-1Q) /CSM_Contig/Contig-U05667-1Q.Seq.d
         (434 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116920_8(AC116920|pid:none) Dictyostelium discoideum chromosom...   102   5e-21
AF211133_1(AF211133|pid:none) Carsonella ruddii natural-host Cte...    34   1.8
CR382135_162(CR382135|pid:none) Debaryomyces hansenii strain CBS...    34   1.8
(Q057X9) RecName: Full=Isoleucyl-tRNA synthetase;          EC=6....    32   6.9
AF165818_95(AF165818|pid:none) Guillardia theta nucleomorph chro...    32   9.0
CP001172_3198(CP001172|pid:none) Acinetobacter baumannii AB307-0...    32   9.0

>AC116920_8(AC116920|pid:none) Dictyostelium discoideum chromosome 2
           map 4415041-4520361 strain AX4, complete sequence.
          Length = 63

 Score =  102 bits (253), Expect = 5e-21
 Identities = 54/64 (84%), Positives = 58/64 (90%)
 Frame = +1

Query: 46  ILGSISTFSQFNVKKSKSKNDSITLFLKSNVVGYTNSMVSQIDGRFDNIPQISQKPPNKP 225
           ILGSISTFSQFNVKKSK  NDSI+ FLKSNV GY+NSMVS+IDGRFDN+P I QKPPNKP
Sbjct: 3   ILGSISTFSQFNVKKSK--NDSISSFLKSNV-GYSNSMVSEIDGRFDNLPIIIQKPPNKP 59

Query: 226 NAYI 237
           NAYI
Sbjct: 60  NAYI 63

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: 515,063,562
Number of extensions: 9090033
Number of successful extensions: 26723
Number of sequences better than 10.0: 6
Number of HSP's gapped: 26717
Number of HSP's successfully gapped: 6
Length of query: 144
Length of database: 1,040,966,779
Length adjustment: 107
Effective length of query: 37
Effective length of database: 698,108,284
Effective search space: 25830006508
Effective search space used: 25830006508
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: 0.70  gvh: 0.48  alm: 0.48  top: 0.53  tms: 0.00  mit: 0.41  mip: 0.00
 nuc: 0.24  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 

	 52.0 %: nuclear
	 20.0 %: mitochondrial
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: plasma membrane
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U05667-1 is nuc
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 3
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