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Dicty_cDB
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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-U09480-1
Contig ID Contig-U09480-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U09480-1 (Contig-U09480-1Q) /CSM_Contig/Contig-U09480-1Q.Seq.d
ATAATAATAATAATAATAATAATAATAATAATAATAATAATAATAAATAA
TGGCAGAAATTAATATTGAGAATCCATTTCATGTTAATACAAAAATCGAT
GTAAATACATTTGTTAATCAAATTAGAGGAATTCCAAATGGTTCTCGTTG
TGATTTTACAAATAGTGTGGTAAAACATTTCTCATCATTAGGTTATAATG
TTTTTGTTTGTCATCCAAATCATGCTGTCACAGGTCCATATGCTAAACTC
CATTGTGAATTTAGAAATACAAAATTTTCAACAATTGGCTATGATGTTTA
TATAATCGCCAGAGGTCGTAAAGTTACTGCAACTAATTTTGGTGATGGTG
GTTATGATAATTGGGCATCCGGTGGTCATTATAATCAAGCAGGTAAAACA
ATAAATTTTCTCTAATCCTTTTTCTTTCATTATTTATTTCAATTTTTGTG
TATATATAGATGTATATATTTTAAAAAATTATTTCAATAATTTTTTTAAA
ATCCAAACATTTAATTATAATTGTATATTTTTAAAAAAAAAATAAT----
------AAATAATAATAATAATAATAATAATAATAAAATAATAGGGAAAA
TCAAATACAATTGTAAATTAAAAATTTAAATAAATTTTTTTTTTTTTTTT
TTATTTTTTTATTTCTTTAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAA
AAAAAAAAAAAAAAA
Gap gap included
Contig length 705
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 4277527
End point 4276817
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 2
Link to clone list U09480
List of clone(s) 

est1=SSL125F,1,547
est2=SSL125Z,548,707
Translated Amino Acid sequence 
***************imaeinienpfhvntkidvntfvnqirgipngsrcdftnsvvkhf
sslgynvfvchpnhavtgpyaklhcefrntkfstigydvyiiargrkvtatnfgdggydn
wasgghynqagktinfl*sfffhylfqflciyrciyfkklfq*ff*npni*l*LYIFKKK
I---

---NNNNNNNNNKIIGKIKYNCKLKI*inffffflffyffkqkkkkkkkkkkkkk
Translated Amino Acid sequence (All Frames) 
Frame A:
iiiiiiiiiiiiiiinngrn*y*esisc*yknrckyic*sn*rnskwfsl*fyk*cgktf
liirl*cfclsskscchrsic*tpl*i*kykifnnwl*clynrqrs*sycn*fw*wwl**
lgirwsl*ssr*nnkfslilflslfisifvyi*myif*kiisiiflkskhliiivyf*kk
nn---

---k*********nnrenqiql*iknlnkffffffiflfl*tkkkkkkkkkkkkkk

Frame B:
***************imaeinienpfhvntkidvntfvnqirgipngsrcdftnsvvkhf
sslgynvfvchpnhavtgpyaklhcefrntkfstigydvyiiargrkvtatnfgdggydn
wasgghynqagktinfl*sfffhylfqflciyrciyfkklfq*ff*npni*l*LYIFKKK
I---

---NNNNNNNNNKIIGKIKYNCKLKI*inffffflffyffkqkkkkkkkkkkkkk

Frame C:
nnnnnnnnnnnnnnk*wqklilrihfmliqksm*ihllikleefqmvlvvilqivw*nis
hh*vimflfviqimlsqvhmlnsivnleiqnfqqlammfi*spevvkllqlilvmvvmii
ghpvviiikqvkq*ifsnpfsfiiyfnfcvyidvyilknyfnnffkiqtfnynciflkkk
*---

---iiiiiiiiik**gksntivn*kfk*ifffffyffislnkkkkkkkkkkkkkk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U09480-1 (Contig-U09480-1Q)
/CSM_Contig/Contig-U09480-1Q.Seq.d
         (715 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U09480-1 (Contig-U09480-1Q) /CSM_Contig/Conti...   912  0.0
Contig-U11432-1 (Contig-U11432-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U12084-1 (Contig-U12084-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U05646-1 (Contig-U05646-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U04515-1 (Contig-U04515-1Q) /CSM_Contig/Conti...    38  0.013
Contig-U13903-1 (Contig-U13903-1Q) /CSM_Contig/Conti...    36  0.050
Contig-U12855-1 (Contig-U12855-1Q) /CSM_Contig/Conti...    36  0.050
Contig-U09506-1 (Contig-U09506-1Q) /CSM_Contig/Conti...    36  0.050
Contig-U05231-1 (Contig-U05231-1Q) /CSM_Contig/Conti...    36  0.050
Contig-U01734-1 (Contig-U01734-1Q) /CSM_Contig/Conti...    36  0.050

>Contig-U09480-1 (Contig-U09480-1Q) /CSM_Contig/Contig-U09480-1Q.Seq.d
          Length = 715

 Score =  912 bits (460), Expect = 0.0
 Identities = 474/481 (98%)
 Strand = Plus / Plus

                                                                       
Query: 52  ggcagaaattaatattgagaatccatttcatgttaatacaaaaatcgatgtaaatacatt 111
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52  ggcagaaattaatattgagaatccatttcatgttaatacaaaaatcgatgtaaatacatt 111

                                                                       
Query: 112 tgttaatcaaattagaggaattccaaatggttctcgttgtgattttacaaatagtgtggt 171
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 112 tgttaatcaaattagaggaattccaaatggttctcgttgtgattttacaaatagtgtggt 171

                                                                       
Query: 172 aaaacatttctcatcattaggttataatgtttttgtttgtcatccaaatcatgctgtcac 231
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 172 aaaacatttctcatcattaggttataatgtttttgtttgtcatccaaatcatgctgtcac 231

                                                                       
Query: 232 aggtccatatgctaaactccattgtgaatttagaaatacaaaattttcaacaattggcta 291
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 232 aggtccatatgctaaactccattgtgaatttagaaatacaaaattttcaacaattggcta 291

                                                                       
Query: 292 tgatgtttatataatcgccagaggtcgtaaagttactgcaactaattttggtgatggtgg 351
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 292 tgatgtttatataatcgccagaggtcgtaaagttactgcaactaattttggtgatggtgg 351

                                                                       
Query: 352 ttatgataattgggcatccggtggtcattataatcaagcaggtaaaacaataaattttct 411
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 352 ttatgataattgggcatccggtggtcattataatcaagcaggtaaaacaataaattttct 411

                                                                       
Query: 412 ctaatcctttttctttcattatttatttcaatttttgtgtatatatagatgtatatattt 471
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 412 ctaatcctttttctttcattatttatttcaatttttgtgtatatatagatgtatatattt 471

                                                                       
Query: 472 taaaaaattatttcaataannnnnnnaaaatccaaacatttaattataattgtatatttt 531
           |||||||||||||||||||       ||||||||||||||||||||||||||||||||||
Sbjct: 472 taaaaaattatttcaataatttttttaaaatccaaacatttaattataattgtatatttt 531

            
Query: 532 t 532
           |
Sbjct: 532 t 532


 Score = 81.8 bits (41), Expect = 9e-16
 Identities = 41/41 (100%)
 Strand = Plus / Plus

                                                    
Query: 594 gggaaaatcaaatacaattgtaaattaaaaatttaaataaa 634
           |||||||||||||||||||||||||||||||||||||||||
Sbjct: 594 gggaaaatcaaatacaattgtaaattaaaaatttaaataaa 634


>Contig-U11432-1 (Contig-U11432-1Q) /CSM_Contig/Contig-U11432-1Q.Seq.d
          Length = 2068

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 20/20 (100%)
 Strand = Plus / Plus

                                
Query: 615  aaattaaaaatttaaataaa 634
            ||||||||||||||||||||
Sbjct: 2031 aaattaaaaatttaaataaa 2050


>Contig-U12084-1 (Contig-U12084-1Q) /CSM_Contig/Contig-U12084-1Q.Seq.d
          Length = 1343

 Score = 38.2 bits (19), Expect = 0.013
 Identities = 22/23 (95%)
 Strand = Plus / Minus

                                  
Query: 92  aaaatcgatgtaaatacatttgt 114
           ||||||||||||| |||||||||
Sbjct: 721 aaaatcgatgtaattacatttgt 699


  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: 13,543
Number of Sequences: 6905
Number of extensions: 13543
Number of successful extensions: 1582
Number of sequences better than 10.0: 211
length of query: 715
length of database: 5,674,871
effective HSP length: 16
effective length of query: 699
effective length of database: 5,564,391
effective search space: 3889509309
effective search space used: 3889509309
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2008.11.16
Homology vs DNA 
Query= Contig-U09480-1 (Contig-U09480-1Q) /CSM_Contig/Contig-U09480-1Q.Seq.d
         (715 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

(AU074495) Dictyostelium discoideum slug cDNA, clone SSL125.      375   2e-99  1
(CR812918) Zebrafish DNA sequence from clone CH211-278P11 in...    48   0.46   1
(AC194675) Zea mays chromosome 5 clone CH201-514D4; ZMMBBc05...    48   0.46   1
(AC185310) Zea mays chromosome 5 clone CH201-326M13; ZMMBBc0...    48   0.46   1
(CL447284) ZMMBBb0468M10f ZMMBBb (HindIII) Zea mays subsp. m...    48   0.46   1
(CL393412) ZMMBBb0199A15r ZMMBBb (HindIII) Zea mays subsp. m...    48   0.46   1
(BZ721918) PUBNV67TD ZM_0.6_1.0_KB Zea mays genomic clone ZM...    48   0.46   1
(BX547933) Zebrafish DNA sequence from clone DKEY-87L9 in li...    34   3.5    2
(EJ325080) 1092351328311 Global-Ocean-Sampling_GS-28-01-01-1...    34   4.7    2
(EJ188979) 1092344174418 Global-Ocean-Sampling_GS-27-01-01-1...    32   6.2    3
(AE014298) Drosophila melanogaster chromosome X, complete se...    44   7.1    1
(AC130390) Drosophila melanogaster X BAC RP98-21O19 (Roswell...    44   7.1    1
(AC104607) Drosophila melanogaster X BAC RP98-19G9 (Roswell ...    44   7.1    1
(AC231905) Choloepus hoffmanni clone CH281-404G3, WORKING DR...    44   7.1    1
(AC231567) Choloepus hoffmanni clone CH281-36G8, WORKING DRA...    44   7.1    1
(AC231308) Choloepus hoffmanni clone CH281-217F13, WORKING D...    44   7.1    1
(AC014182) Drosophila melanogaster, *** SEQUENCING IN PROGRE...    44   7.1    1
(AC180089) Strongylocentrotus purpuratus clone R3-4008L4, WO...    38   7.7    2

>(AU074495) Dictyostelium discoideum slug cDNA, clone SSL125.
          Length = 240

 Score =  375 bits (189), Expect = 2e-99
 Identities = 189/189 (100%)
 Strand = Plus / Plus


Query: 52  ggcagaaattaatattgagaatccatttcatgttaatacaaaaatcgatgtaaatacatt 111
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 52  ggcagaaattaatattgagaatccatttcatgttaatacaaaaatcgatgtaaatacatt 111


Query: 112 tgttaatcaaattagaggaattccaaatggttctcgttgtgattttacaaatagtgtggt 171
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 112 tgttaatcaaattagaggaattccaaatggttctcgttgtgattttacaaatagtgtggt 171


Query: 172 aaaacatttctcatcattaggttataatgtttttgtttgtcatccaaatcatgctgtcac 231
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 172 aaaacatttctcatcattaggttataatgtttttgtttgtcatccaaatcatgctgtcac 231


Query: 232 aggtccata 240
           |||||||||
Sbjct: 232 aggtccata 240

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 484,335,834
Number of extensions: 32511091
Number of successful extensions: 2416772
Number of sequences better than 10.0: 19
Length of query: 715
Length of database: 95,242,211,685
Length adjustment: 24
Effective length of query: 691
Effective length of database: 97,308,875,965
Effective search space: 67240433291815
Effective search space used: 67240433291815
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 6.26
Homology vs Protein 
Query= Contig-U09480-1 (Contig-U09480-1Q) /CSM_Contig/Contig-U09480-1Q.Seq.d
         (715 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000813_737(CP000813|pid:none) Bacillus pumilus SAFR-032, compl...    38   0.27
(O32211) RecName: Full=Stress response protein yvgO; Flags: Prec...    37   0.60
AE017333_2145(AE017333|pid:none) Bacillus licheniformis DSM 13, ...    36   1.3
EF429087_1(EF429087|pid:none) Streptomyces fradiae clone k11 lip...    33   6.6

>CP000813_737(CP000813|pid:none) Bacillus pumilus SAFR-032, complete
           genome.
          Length = 170

 Score = 38.1 bits (87), Expect = 0.27
 Identities = 32/117 (27%), Positives = 51/117 (43%), Gaps = 7/117 (5%)
 Frame = +2

Query: 80  HVNTKIDV----NTFVNQIRGIPNGSRCDFTNSVVKH-FSSLG--YNVFVCHPNHAVTGP 238
           +VN   DV    N  VN +    N +R  F   V++  F + G  YNV V + +
Sbjct: 57  NVNVNFDVLGIANAIVNAVNS--NANRPGFVKGVMESTFYAAGGRYNVMVFNLSQNYEDR 114

Query: 239 YAKLHCEFRNTKFSTIGYDVYIIARGRKVTATNFGDGGYDNWASGGHYNQAGKTINF 409
           +  +   F       + Y +++   G   T  N G GG+DNWA  G +++  K + F
Sbjct: 115 FNGVKT-FATANLGNVVYGIWVFESG---TFKNNGHGGWDNWAFRGWFDRQDKFVTF 167

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: 825,692,002
Number of extensions: 14834865
Number of successful extensions: 29746
Number of sequences better than 10.0: 4
Number of HSP's gapped: 29713
Number of HSP's successfully gapped: 4
Length of query: 238
Length of database: 1,040,966,779
Length adjustment: 125
Effective length of query: 113
Effective length of database: 640,431,154
Effective search space: 72368720402
Effective search space used: 72368720402
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: 31 (16.5 bits)
PSORT 

 psg: 0.44  gvh: -0.15  alm: 0.70  top: 0.53  tms: 0.00  mit: 0.38  mip: 0.00
 nuc: 0.12  erl: 0.00  erm: 0.40  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 

	 80.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: mitochondrial

>> prediction for Contig-U09480-1 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) 1
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