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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-U04992-1
Contig ID Contig-U04992-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04992-1 (Contig-U04992-1Q) /CSM_Contig/Contig-U04992-1Q.Seq.d
CATAATTTCTCCTATACAAATATTTTTTGTATAGTTGTCATTTGTAATTT
TTTTTTTTTTTTTTCTTTTTAAAAAAAAAAATAAAAAAATCTTTTTTTTT
TTTATTTTATTTTAAATCAGTCCTCCAAATTTTTGTATCATTAGTTATAT
AATAATTATTTTATTTTATTTTTTATAAAAAAAATAACACAATGACAGTT
TTAAATAAAATAAAAACTTCAATTAAAAATTTCCATATCAAAGATATTAG
TCCAATTAAAAAGGNTGAAAAAAGAGAAAGATATTTAATTTTTGGAACTT
CTTTTCCTCATTTTGCAAGAATGCTTGGAGTAATTTTACTTTTATGGGCA
GTTTTCATATCAATGTTTTTAGGTTTATTACATGGTTATACTNGAAATAA
AAATCAATTTAAAGCAACTGCTCTTTTAAAAAAAAATATAAAAAATAAAA
AAAATTTATAAAACAAANTAAAAAAAAAAAAAAAAAGAGACAACCCCTTT
ATTATATTTTAGAGGGTATTTATATAAAAAAAA
Gap no gap
Contig length 533
Chromosome number (1..6, M) 1
Chromosome length 4919822
Start point 1307469
End point 1306928
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U04992
List of clone(s) 

est1=SSE373E,1,534
Translated Amino Acid sequence 
*fllykyflyschl*ffffffflkkkikksffflfyfksvlqifvslvi**LFYFIFYKK
NNTMTVLNKIKTSIKNFHIKDISPIKKXEKRERYLIFGTSFPHFARMLGVILLLWAVFIS
MFLGLLHGYTXNKNQFKATALLKKNIKNKKNL*nkxkkkkkrdnpfiif*rvfi*kk
Translated Amino Acid sequence (All Frames) 
Frame A:
hnfsytnifcivvicnfffffsf*kkk*knlfffyfilnqsskflyh*lynnyfilffik
kitq*qf*ik*klqlkisiskilvqlkrxkkekdi*flellflilqecle*fyfygqfsy
qcf*vyymvileikinlkqllf*kki*kikkiyktx*kkkkkettpllyfrgylykk


Frame B:
iispiqiffv*lsfviffffflfkkknkkiffffilf*isppnfciisyiiiilfyfl*k
k*hndsfk*nknfn*kfpyqry*sn*kg*kkrkifnfwnffssfcknawsnftfmgsfhi
nvfrfitwlyxk*ksi*sncsfkkkykk*kkfikqxkkkkkkrqplyyilegiyikk


Frame C:
*fllykyflyschl*ffffffflkkkikksffflfyfksvlqifvslvi**LFYFIFYKK
NNTMTVLNKIKTSIKNFHIKDISPIKKXEKRERYLIFGTSFPHFARMLGVILLLWAVFIS
MFLGLLHGYTXNKNQFKATALLKKNIKNKKNL*nkxkkkkkrdnpfiif*rvfi*kk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04992-1 (Contig-U04992-1Q)
/CSM_Contig/Contig-U04992-1Q.Seq.d
         (533 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04992-1 (Contig-U04992-1Q) /CSM_Contig/Conti...   583  e-167
Contig-U05530-1 (Contig-U05530-1Q) /CSM_Contig/Conti...   113  2e-25
Contig-U10201-1 (Contig-U10201-1Q) /CSM_Contig/Conti...    48  1e-05
Contig-U14651-1 (Contig-U14651-1Q) /CSM_Contig/Conti...    46  4e-05
Contig-U12269-1 (Contig-U12269-1Q) /CSM_Contig/Conti...    44  2e-04
Contig-U09694-1 (Contig-U09694-1Q) /CSM_Contig/Conti...    44  2e-04
Contig-U01396-1 (Contig-U01396-1Q) /CSM_Contig/Conti...    44  2e-04
Contig-U14786-1 (Contig-U14786-1Q) /CSM_Contig/Conti...    42  6e-04
Contig-U12817-1 (Contig-U12817-1Q) /CSM_Contig/Conti...    42  6e-04
Contig-U11787-1 (Contig-U11787-1Q) /CSM_Contig/Conti...    42  6e-04

>Contig-U04992-1 (Contig-U04992-1Q) /CSM_Contig/Contig-U04992-1Q.Seq.d
          Length = 533

 Score =  583 bits (294), Expect = e-167
 Identities = 316/324 (97%)
 Strand = Plus / Plus

                                                                       
Query: 104 attttattttaaatcagtcctccaaatttttgtatcattagttatataataattatttta 163
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 104 attttattttaaatcagtcctccaaatttttgtatcattagttatataataattatttta 163

                                                                       
Query: 164 ttttattttttatnnnnnnnntaacacaatgacagttttaaataaaataaaaacttcaat 223
           |||||||||||||        |||||||||||||||||||||||||||||||||||||||
Sbjct: 164 ttttattttttataaaaaaaataacacaatgacagttttaaataaaataaaaacttcaat 223

                                                                       
Query: 224 taaaaatttccatatcaaagatattagtccaattaaaaaggntgaaaaaagagaaagata 283
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 224 taaaaatttccatatcaaagatattagtccaattaaaaaggntgaaaaaagagaaagata 283

                                                                       
Query: 284 tttaatttttggaacttcttttcctcattttgcaagaatgcttggagtaattttactttt 343
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 284 tttaatttttggaacttcttttcctcattttgcaagaatgcttggagtaattttactttt 343

                                                                       
Query: 344 atgggcagttttcatatcaatgtttttaggtttattacatggttatactngaaataaaaa 403
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 344 atgggcagttttcatatcaatgtttttaggtttattacatggttatactngaaataaaaa 403

                                   
Query: 404 tcaatttaaagcaactgctctttt 427
           ||||||||||||||||||||||||
Sbjct: 404 tcaatttaaagcaactgctctttt 427


 Score = 93.7 bits (47), Expect = 2e-19
 Identities = 47/47 (100%)
 Strand = Plus / Plus

                                                         
Query: 1  cataatttctcctatacaaatattttttgtatagttgtcatttgtaa 47
          |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  cataatttctcctatacaaatattttttgtatagttgtcatttgtaa 47


 Score = 77.8 bits (39), Expect = 1e-14
 Identities = 39/39 (100%)
 Strand = Plus / Plus

                                                  
Query: 487 gagacaacccctttattatattttagagggtatttatat 525
           |||||||||||||||||||||||||||||||||||||||
Sbjct: 487 gagacaacccctttattatattttagagggtatttatat 525


 Score = 28.2 bits (14), Expect = 9.0
 Identities = 14/14 (100%)
 Strand = Plus / Minus

                         
Query: 203 aaataaaataaaaa 216
           ||||||||||||||
Sbjct: 112 aaataaaataaaaa 99


 Score = 28.2 bits (14), Expect = 9.0
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 159 ttttattttatttt 172
           ||||||||||||||
Sbjct: 100 ttttattttatttt 113


>Contig-U05530-1 (Contig-U05530-1Q) /CSM_Contig/Contig-U05530-1Q.Seq.d
          Length = 428

 Score =  113 bits (57), Expect = 2e-25
 Identities = 81/89 (91%)
 Strand = Plus / Plus

                                                                       
Query: 288 atttttggaacttcttttcctcattttgcaagaatgcttggagtaattttacttttatgg 347
           ||||| || ||||||||||||||||||||  |||||||||| |||||||| |||||||||
Sbjct: 138 attttggggacttcttttcctcattttgctggaatgcttggggtaattttccttttatgg 197

                                        
Query: 348 gcagttttcatatcaatgtttttaggttt 376
           || |||||||||||||||||||| |||||
Sbjct: 198 gcggttttcatatcaatgtttttgggttt 226


 Score = 50.1 bits (25), Expect = 2e-06
 Identities = 34/37 (91%)
 Strand = Plus / Plus

                                                
Query: 489 gacaacccctttattatattttagagggtatttatat 525
           |||||||||||||||||||||| | |||| |||||||
Sbjct: 337 gacaacccctttattatattttggggggtttttatat 373


>Contig-U10201-1 (Contig-U10201-1Q) /CSM_Contig/Contig-U10201-1Q.Seq.d
          Length = 1179

 Score = 48.1 bits (24), Expect = 1e-05
 Identities = 27/28 (96%)
 Strand = Plus / Minus

                                        
Query: 145  ttatataataattattttattttatttt 172
            |||| |||||||||||||||||||||||
Sbjct: 1158 ttatttaataattattttattttatttt 1131


 Score = 42.1 bits (21), Expect = 6e-04
 Identities = 21/21 (100%)
 Strand = Plus / Minus

                                 
Query: 156  ttattttattttattttttat 176
            |||||||||||||||||||||
Sbjct: 1137 ttattttattttattttttat 1117


 Score = 34.2 bits (17), Expect = 0.15
 Identities = 17/17 (100%)
 Strand = Plus / Minus

                             
Query: 156  ttattttattttatttt 172
            |||||||||||||||||
Sbjct: 1142 ttattttattttatttt 1126


  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: 20,908
Number of Sequences: 6905
Number of extensions: 20908
Number of successful extensions: 5732
Number of sequences better than 10.0: 1338
length of query: 533
length of database: 5,674,871
effective HSP length: 16
effective length of query: 517
effective length of database: 5,564,391
effective search space: 2876790147
effective search space used: 2876790147
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 2009. 7. 6
Homology vs DNA 
Query= Contig-U04992-1 (Contig-U04992-1Q) /CSM_Contig/Contig-U04992-1Q.Seq.d
         (533 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

(AU037854) Dictyostelium discoideum slug cDNA, clone SSE373.      315   e-118  3
(C90950) Dictyostelium discoideum slug cDNA, clone SSJ345.        113   1e-28  2
(CP001287) Cyanothece sp. PCC 8801, complete genome.               38   0.17   2
(CR382400) Plasmodium falciparum chromosome 6, complete sequ...    48   0.34   1
(CT827851) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    46   1.4    1
(EH099481) ia176h11.x1 mouse taste receptor cell, subtracted...    46   1.4    1
(AC142872) Macaca mulatta clone CH250-271F13, *** SEQUENCING...    34   2.7    2
(AL159985) Human DNA sequence from clone RP11-22L21 on chrom...    40   4.1    2
(AC125217) Mus musculus BAC clone RP23-112D14 from 8, comple...    36   4.4    3
(AC068766) Homo sapiens chromosome 3 clone RP11-84J20, WORKI...    36   5.0    4
(AC114561) Mus musculus chromosome 6, clone RP23-54F12, comp...    44   5.4    1
(AC113206) Mus musculus chromosome 6, clone RP23-320B19, com...    44   5.4    1
(AC090355) Homo sapiens chromosome 18, clone RP11-745C22, co...    44   5.4    1
(AC105559) Rattus norvegicus clone CH230-228F12, WORKING DRA...    44   5.4    1
(FP236376) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    44   5.4    1
(AP001563) Homo sapiens genomic DNA, chromosome 18q12 clone:...    44   5.4    1
(AC169221) Bos taurus clone CH240-216M2, WORKING DRAFT SEQUE...    44   5.4    1
(AC013659) Homo sapiens clone RP11-20A13, WORKING DRAFT SEQU...    44   5.4    1
(FI196225) CccaBa025-L14TR CccABa Cajanus cajan genomic clon...    44   5.4    1
(EB237306) PEG003-C-222759-501 Normalized Pedal-Pleural Gang...    44   5.4    1
(CX430589) JGI_XZG61689.rev NIH_XGC_tropGas7 Xenopus (Silura...    44   5.4    1
(DQ780080) Endoriftia persephone 'Hot96_1+Hot96_2' clone rif...    44   5.4    1
(AC144484) Medicago truncatula clone mth2-30o16, complete se...    34   5.4    7
(AL162577) Human DNA sequence *** SEQUENCING CANCELLED *** f...    40   5.7    2
(AC112492) Homo sapiens X BAC RP11-12D5 (Roswell Park Cancer...    38   6.7    5
(AC174341) Medicago truncatula chromosome 8 clone mth2-165f2...    38   7.4    5
(AX346723) Sequence 1794 from Patent WO0200928.                    36   8.4    2
(FH367370) CHO_OF4502xc07r1.ab1 CHO_OF4 Nicotiana tabacum ge...    38   8.5    2
(EJ953630) 1093018960827 Global-Ocean-Sampling_GS-30-02-01-1...    34   9.4    2
(AC164277) Bos taurus clone CH240-132N12, *** SEQUENCING IN ...    32   9.4    2
(AC182890) Bos taurus clone CH240-526L24, WORKING DRAFT SEQU...    32   9.7    2
(AZ690281) ENTGV88TR Entamoeba histolytica Sheared DNA Entam...    38   9.8    2

>(AU037854) Dictyostelium discoideum slug cDNA, clone SSE373.
          Length = 534

 Score =  315 bits (159), Expect(3) = e-118
 Identities = 162/162 (100%)
 Strand = Plus / Plus


Query: 266 tgaaaaaagagaaagatatttaatttttggaacttcttttcctcattttgcaagaatgct 325
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 266 tgaaaaaagagaaagatatttaatttttggaacttcttttcctcattttgcaagaatgct 325


Query: 326 tggagtaattttacttttatgggcagttttcatatcaatgtttttaggtttattacatgg 385
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 326 tggagtaattttacttttatgggcagttttcatatcaatgtttttaggtttattacatgg 385


Query: 386 ttatactngaaataaaaatcaatttaaagcaactgctctttt 427
           ||||||||||||||||||||||||||||||||||||||||||
Sbjct: 386 ttatactngaaataaaaatcaatttaaagcaactgctctttt 427

 Score = 93.7 bits (47), Expect(3) = e-118
 Identities = 47/47 (100%)
 Strand = Plus / Plus


Query: 1  cataatttctcctatacaaatattttttgtatagttgtcatttgtaa 47
          |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1  cataatttctcctatacaaatattttttgtatagttgtcatttgtaa 47

 Score = 77.8 bits (39), Expect(3) = e-118
 Identities = 39/39 (100%)
 Strand = Plus / Plus


Query: 487 gagacaacccctttattatattttagagggtatttatat 525
           |||||||||||||||||||||||||||||||||||||||
Sbjct: 487 gagacaacccctttattatattttagagggtatttatat 525

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 414,293,635
Number of extensions: 29056877
Number of successful extensions: 2539018
Number of sequences better than 10.0: 32
Length of query: 533
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 510
Effective length of database: 99,442,330,388
Effective search space: 50715588497880
Effective search space used: 50715588497880
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.31
Homology vs Protein 
Query= Contig-U04992-1 (Contig-U04992-1Q) /CSM_Contig/Contig-U04992-1Q.Seq.d
         (533 letters)

Database: nrp_A
           3,268,448 sequences; 1,061,185,681 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000916_662(CP000916|pid:none) Thermotoga neapolitana DSM 4359,...    35   1.2
(Q3TZM9) RecName: Full=Asparagine-linked glycosylation protein 1...    33   6.0

>CP000916_662(CP000916|pid:none) Thermotoga neapolitana DSM 4359,
           complete genome.
          Length = 273

 Score = 35.0 bits (79), Expect = 1.2
 Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 2/70 (2%)
 Frame = +3

Query: 210 IKTSIKNFHIKDISPIKKXEKRERYLIFGTSFPHFARML--GVILLLWAVFISMFLGLLH 383
           + TS+KNF    IS + K   R  +  F  +F      L    +L++ A  IS FLG ++
Sbjct: 29  LATSLKNFEEVSISTMWKLPTRISFDGFIEAFQKLKMNLKNSFLLVIPATLISSFLGSIN 88

Query: 384 GYTXNKNQFK 413
           GY  +K +FK
Sbjct: 89  GYVFSKVRFK 98

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: 3268448
Number of Hits to DB: 485,679,953
Number of extensions: 6326588
Number of successful extensions: 21336
Number of sequences better than 10.0: 2
Number of HSP's gapped: 21330
Number of HSP's successfully gapped: 2
Length of query: 177
Length of database: 1,061,185,681
Length adjustment: 120
Effective length of query: 57
Effective length of database: 668,971,921
Effective search space: 38131399497
Effective search space used: 38131399497
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: 30 (16.2 bits)
PSORT 

 psg: 0.72  gvh: 0.41  alm: 0.17  top: 0.60  tms: 0.07  mit: 0.34  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.80  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  tyr: 0.12  leu: 0.35  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 1.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 28.0 %: cytoplasmic
	 24.0 %: mitochondrial
	 24.0 %: nuclear
	  8.0 %: plasma membrane
	  8.0 %: endoplasmic reticulum
	  4.0 %: vesicles of secretory system
	  4.0 %: peroxisomal

>> prediction for Contig-U04992-1 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) 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