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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-U13305-1
Contig ID Contig-U13305-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13305-1 (Contig-U13305-1Q) /CSM_Contig/Contig-U13305-1Q.Seq.d
NNNNNNNNNNATTATTTTTCAAAACCTTTCANATTTAAANTGGGATTTAT
CTTGGGATTTTGCAATTAANATGTTAACANTGGTTGGNACTGTTTGGGGT
TTTGAANTTTTAGTTGANGCGATCAAACANGNTTTTATCNCTAAATTCAA
NAAATTTTCCCCNCAAANGNATTCAAAATTNTTTGNACTTTTATCCGANA
CAANAGNTGACCCAANGAANANAAATTTCNCTGAAAGTTCANGGGGNGNA
AANAANANAANTGGNTTTGGACCNTTTCCNTTANNTTCAATTGTTGTAAN
AGTATTTNANAAATTCNTTCCNTCAAAANGNATTTTTGGNANATTTTTAA
NGGNTCAAANTTANANANGTNTTGNACTTTTAAAAANATTTATAAAAATC
NTTATCCTCGGNCAATGTTTATCAAAAACCCCCNATTATGATAACCCNAC
NACAACTATTTTATCATCATCATCATTTTNATCATCATCAAATTCATTAA
ANACCCCTTCAACAACATCAACCNCAACTTCAACAACNAAANATAAAAAA
AACNATTAAAANAAAAAAAAAAATTAAAAATAAAAATAAACGAAAAGAGG
CAATC
Gap no gap
Contig length 605
Chromosome number (1..6, M) -
Chromosome length -
Start point -
End point -
Strand (PLUS/MINUS) -
Number of clones 1
Number of EST 1
Link to clone list U13305
List of clone(s) 

est1=SHL353Z,1,596
Translated Amino Acid sequence 
XXXIIFQNLSXLXWDLSWDFAIXMLTXVGTVWGFEXLVXAIKXXFIXKFXKFSPQXXSKX
FXLLSXTXXDPXXXNFXESSXGXXXXXGFGPFPLXSIVVXVFXKFXPSKXIFGXFLXXQX
XXXXXLLKXFIKIXILGQCLSKTPXYDNPTTTILSSSSFXSSSNSLXTPSTTSTXTSTTK
XKKNX*xkkkn*k*k*tkrgn
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxyfskpfxfkxgfilgfcn*xvnxgwxclgf*xfs*xdqtxfyx*iqxifpxxxfki
xxtfirxxx*pxexkfx*kfxgxkxxxwxwtxsxxfnccxsixxixsxkxxfwxifxgsx
lxxxxtfkxiyknxyprxmfiknpxl**pxxnyfiiiiixiiikfikxpfnninxnfnnx
x*kkxlkxkkklkikinekrq


Frame B:
XXXIIFQNLSXLXWDLSWDFAIXMLTXVGTVWGFEXLVXAIKXXFIXKFXKFSPQXXSKX
FXLLSXTXXDPXXXNFXESSXGXXXXXGFGPFPLXSIVVXVFXKFXPSKXIFGXFLXXQX
XXXXXLLKXFIKIXILGQCLSKTPXYDNPTTTILSSSSFXSSSNSLXTPSTTSTXTSTTK
XKKNX*xkkkn*k*k*tkrgn


Frame C:
xxxlffktfxi*xgiylgilqlxc*xwlxlfgvlxf*lxrsnxxlslnsxnfpxkxiqnx
lxfypxqxxtqxxxislkvxgxxxxxxxldxfxxxqll*xyxxnsfxqxxflxxf*xxkx
xxvlxf*kxl*kslssxnvyqkppimitxxqlfyhhhhfxhhqih*xplqqhqpqlqqxx
ikktikxkkkiknknkrkeai
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13305-1 (Contig-U13305-1Q)
/CSM_Contig/Contig-U13305-1Q.Seq.d
         (605 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13305-1 (Contig-U13305-1Q) /CSM_Contig/Conti...   551  e-157
Contig-U11786-1 (Contig-U11786-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U14885-1 (Contig-U14885-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U12535-1 (Contig-U12535-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U10756-1 (Contig-U10756-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U09903-1 (Contig-U09903-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U09456-1 (Contig-U09456-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U03186-1 (Contig-U03186-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U01212-1 (Contig-U01212-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U12168-1 (Contig-U12168-1Q) /CSM_Contig/Conti...    32  0.66

>Contig-U13305-1 (Contig-U13305-1Q) /CSM_Contig/Contig-U13305-1Q.Seq.d
          Length = 605

 Score =  551 bits (278), Expect = e-157
 Identities = 452/452 (100%)
 Strand = Plus / Plus

                                                                       
Query: 11  attatttttcaaaacctttcanatttaaantgggatttatcttgggattttgcaattaan 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 11  attatttttcaaaacctttcanatttaaantgggatttatcttgggattttgcaattaan 70

                                                                       
Query: 71  atgttaacantggttggnactgtttggggttttgaanttttagttgangcgatcaaacan 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 71  atgttaacantggttggnactgtttggggttttgaanttttagttgangcgatcaaacan 130

                                                                       
Query: 131 gnttttatcnctaaattcaanaaattttccccncaaangnattcaaaattntttgnactt 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 131 gnttttatcnctaaattcaanaaattttccccncaaangnattcaaaattntttgnactt 190

                                                                       
Query: 191 ttatccganacaanagntgacccaangaananaaatttcnctgaaagttcanggggngna 250
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 191 ttatccganacaanagntgacccaangaananaaatttcnctgaaagttcanggggngna 250

                                                                       
Query: 251 aanaananaantggntttggaccntttccnttannttcaattgttgtaanagtatttnan 310
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 251 aanaananaantggntttggaccntttccnttannttcaattgttgtaanagtatttnan 310

                                                                       
Query: 311 aaattcnttccntcaaaangnatttttggnanatttttaanggntcaaanttananangt 370
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 311 aaattcnttccntcaaaangnatttttggnanatttttaanggntcaaanttananangt 370

                                                                       
Query: 371 nttgnacttttaaaaanatttataaaaatcnttatcctcggncaatgtttatcaaaaacc 430
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 371 nttgnacttttaaaaanatttataaaaatcnttatcctcggncaatgtttatcaaaaacc 430

                                           
Query: 431 cccnattatgataacccnacnacaactatttt 462
           ||||||||||||||||||||||||||||||||
Sbjct: 431 cccnattatgataacccnacnacaactatttt 462


 Score = 81.8 bits (41), Expect = 8e-16
 Identities = 47/47 (100%)
 Strand = Plus / Plus

                                                          
Query: 491 aattcattaaanaccccttcaacaacatcaaccncaacttcaacaac 537
           |||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 491 aattcattaaanaccccttcaacaacatcaaccncaacttcaacaac 537


>Contig-U11786-1 (Contig-U11786-1Q) /CSM_Contig/Contig-U11786-1Q.Seq.d
          Length = 1383

 Score = 36.2 bits (18), Expect = 0.042
 Identities = 26/29 (89%)
 Strand = Plus / Plus

                                        
Query: 509 tcaacaacatcaaccncaacttcaacaac 537
           |||||||| |||||  |||||||||||||
Sbjct: 293 tcaacaacttcaacttcaacttcaacaac 321


>Contig-U14885-1 (Contig-U14885-1Q) /CSM_Contig/Contig-U14885-1Q.Seq.d
          Length = 277

 Score = 34.2 bits (17), Expect = 0.17
 Identities = 27/31 (87%)
 Strand = Plus / Plus

                                          
Query: 507 cttcaacaacatcaaccncaacttcaacaac 537
           |||| |||||| ||||  |||||||||||||
Sbjct: 31  cttcnacaacaacaacagcaacttcaacaac 61


  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: 2314
Number of Sequences: 6905
Number of extensions: 2314
Number of successful extensions: 318
Number of sequences better than 10.0: 33
length of query: 605
length of database: 5,674,871
effective HSP length: 16
effective length of query: 589
effective length of database: 5,564,391
effective search space: 3277426299
effective search space used: 3277426299
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 2008.12. 7
Homology vs DNA 
Query= Contig-U13305-1 (Contig-U13305-1Q) /CSM_Contig/Contig-U13305-1Q.Seq.d
         (605 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

(BJ408684) Dictyostelium discoideum cDNA clone:dds46j13, 3' ...   321   e-166  3
(BJ382753) Dictyostelium discoideum cDNA clone:ddc45c23, 3' ...   289   e-146  3
(BJ382318) Dictyostelium discoideum cDNA clone:ddc44i12, 3' ...   289   e-146  3
(BJ442891) Dictyostelium discoideum cDNA clone:ddv51d07, 3' ...   289   e-146  3
(BJ380521) Dictyostelium discoideum cDNA clone:ddc38o08, 3' ...   289   e-144  3
(BJ443873) Dictyostelium discoideum cDNA clone:ddv54m10, 3' ...   289   e-144  3
(AC116977) Dictyostelium discoideum chromosome 2 map 5515173...   289   e-131  3
(BJ342777) Dictyostelium discoideum cDNA clone:dda1e14, 3' e...   289   e-130  3
(BJ383581) Dictyostelium discoideum cDNA clone:ddc53d13, 3' ...   281   e-124  3
(BJ383402) Dictyostelium discoideum cDNA clone:ddc52l19, 3' ...   214   e-114  3
(BJ384037) Dictyostelium discoideum cDNA clone:ddc48c06, 3' ...   131   1e-43  2

>(BJ408684) Dictyostelium discoideum cDNA clone:dds46j13, 3' end,
           single read.
          Length = 596

 Score =  321 bits (162), Expect(3) = e-166
 Identities = 231/231 (100%)
 Strand = Plus / Minus


Query: 11  attatttttcaaaacctttcanatttaaantgggatttatcttgggattttgcaattaan 70
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 596 attatttttcaaaacctttcanatttaaantgggatttatcttgggattttgcaattaan 537


Query: 71  atgttaacantggttggnactgtttggggttttgaanttttagttgangcgatcaaacan 130
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 536 atgttaacantggttggnactgtttggggttttgaanttttagttgangcgatcaaacan 477


Query: 131 gnttttatcnctaaattcaanaaattttccccncaaangnattcaaaattntttgnactt 190
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 476 gnttttatcnctaaattcaanaaattttccccncaaangnattcaaaattntttgnactt 417


Query: 191 ttatccganacaanagntgacccaangaananaaatttcnctgaaagttca 241
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 416 ttatccganacaanagntgacccaangaananaaatttcnctgaaagttca 366

 Score =  232 bits (117), Expect(3) = e-166
 Identities = 201/201 (100%)
 Strand = Plus / Minus


Query: 262 tggntttggaccntttccnttannttcaattgttgtaanagtatttnanaaattcnttcc 321
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 345 tggntttggaccntttccnttannttcaattgttgtaanagtatttnanaaattcnttcc 286


Query: 322 ntcaaaangnatttttggnanatttttaanggntcaaanttananangtnttgnactttt 381
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 285 ntcaaaangnatttttggnanatttttaanggntcaaanttananangtnttgnactttt 226


Query: 382 aaaaanatttataaaaatcnttatcctcggncaatgtttatcaaaaacccccnattatga 441
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 225 aaaaanatttataaaaatcnttatcctcggncaatgtttatcaaaaacccccnattatga 166


Query: 442 taacccnacnacaactatttt 462
           |||||||||||||||||||||
Sbjct: 165 taacccnacnacaactatttt 145

 Score = 83.8 bits (42), Expect(3) = e-166
 Identities = 51/51 (100%)
 Strand = Plus / Minus


Query: 491 aattcattaaanaccccttcaacaacatcaaccncaacttcaacaacnaaa 541
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 116 aattcattaaanaccccttcaacaacatcaaccncaacttcaacaacnaaa 66

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 242,089,447
Number of extensions: 13896832
Number of successful extensions: 651294
Number of sequences better than 10.0: 11
Length of query: 605
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 582
Effective length of database: 93,106,754,628
Effective search space: 54188131193496
Effective search space used: 54188131193496
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 6
Homology vs Protein 
Query= Contig-U13305-1 (Contig-U13305-1Q) /CSM_Contig/Contig-U13305-1Q.Seq.d
         (605 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q550C1) RecName: Full=Protein TAPT1 homolog;                         162   5e-39
AC116977_15(AC116977|pid:none) Dictyostelium discoideum chromoso...   162   5e-39

>(Q550C1) RecName: Full=Protein TAPT1 homolog;
          Length = 828

 Score =  162 bits (411), Expect = 5e-39
 Identities = 89/145 (61%), Positives = 89/145 (61%)
 Frame = +2

Query: 11   IIFQNLSXLXWDLSWDFAIXMLTXVGTVWGFEXLVXAIKXXFIXKFXKFSPQXXSKXFXL 190
            IIFQNLS L WDLSWDFAI MLT VGTVWG E LV AIK  FI KF KFSPQ  SK F L
Sbjct: 647  IIFQNLSDLNWDLSWDFAINMLTVVGTVWGSEVLVDAIKHAFITKFNKFSPQMYSKFFVL 706

Query: 191  LSXTXXDPXXXNFXESSXGXXXXXGFGPFPLXSIVVXVFXKFXPSKXIFGXFLXXQXXXX 370
            LS T  DP   NF ESS G     GF PFPL SIVV VF KF PSK IFG FL  Q
Sbjct: 707  LSDTIVDPRNRNFTESSWGVNNIIGFVPFPLASIVVRVFHKFIPSKGIFGIFLMVQIYIC 766

Query: 371  XXXXXXXXXXXXXGQCLSKTPXYDN 445
                         GQCLSKT  YDN
Sbjct: 767  LVLLKIFIKIIILGQCLSKTTNYDN 791

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: 345,512,235
Number of extensions: 6459650
Number of successful extensions: 1336
Number of sequences better than 10.0: 2
Number of HSP's gapped: 1334
Number of HSP's successfully gapped: 2
Length of query: 201
Length of database: 1,051,180,864
Length adjustment: 122
Effective length of query: 79
Effective length of database: 656,320,666
Effective search space: 51849332614
Effective search space used: 51849332614
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: 0.80  gvh: 0.75  alm: 0.40  top: 0.53  tms: 0.00  mit: 0.22  mip: 0.00
 nuc: 0.00  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 

	 28.0 %: cytoplasmic
	 24.0 %: mitochondrial
	 20.0 %: nuclear
	  8.0 %: vacuolar
	  8.0 %: endoplasmic reticulum
	  4.0 %: extracellular, including cell wall
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U13305-1 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) 0
SH (FL, L) 1
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0