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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U13388-1
Contig ID Contig-U13388-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13388-1 (Contig-U13388-1Q) /CSM_Contig/Contig-U13388-1Q.Seq.d
CACCAATCTTTATAATTAAAAAAAAAAAAAAAAAAAAAAAAAATGATAAT
TTTAAAAAGGAATATAGTTTTTTTACTTATAATAATTATTGTTTTAGGTA
TATTTATAGCAACATCAATTGAAATTAAAAATTATAAATTATCACTAAAT
CAAAATAAAAATGAAATTTCAAAAAATCCACCAATTTGGCCAGCACCGTT
CTATGGTCAATTTGGTAATAATTCAATATTAATTTCAAAAGAATTTAATT
TTACAATAATATCTGATTCAACATTATTATTAAATAAAACTTTATCAAAA
TATTATAATTTA
Gap no gap
Contig length 312
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 447685
End point 447997
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U13388
List of clone(s) 

est1=SSB640F,1,313
Translated Amino Acid sequence 
hqsl*LKKKKKKKKMIILKRNIVFLLIIIIVLGIFIATSIEIKNYKLSLNQNKNEISKNP
PIWPAPFYGQFGNNSILISKEFNFTIISDSTLLLNKTLSKYYNL
Translated Amino Acid sequence (All Frames) 
Frame A:
hqsl*LKKKKKKKKMIILKRNIVFLLIIIIVLGIFIATSIEIKNYKLSLNQNKNEISKNP
PIWPAPFYGQFGNNSILISKEFNFTIISDSTLLLNKTLSKYYNL


Frame B:
tnlyn*kkkkkkkk**f*kgi*ffyl**llf*vyl*qhqlklkiinyh*ikikmkfqkih
qfgqhrsmvnlviiqy*fqknlilq*yliqhyy*iklyqniii


Frame C:
pifiikkkkkkkkndnfkkeysfftynnycfryiysnin*n*kl*iitksk*k*nfkkst
nlastvlwsiw**fninfkri*fynni*fniiik*nfikil*f
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13388-1 (Contig-U13388-1Q)
/CSM_Contig/Contig-U13388-1Q.Seq.d
         (312 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13388-1 (Contig-U13388-1Q) /CSM_Contig/Conti...   268  3e-72
Contig-U10839-1 (Contig-U10839-1Q) /CSM_Contig/Conti...    38  0.005
Contig-U14478-1 (Contig-U14478-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U13902-1 (Contig-U13902-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U12496-1 (Contig-U12496-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U11812-1 (Contig-U11812-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U09958-1 (Contig-U09958-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U05676-1 (Contig-U05676-1Q) /CSM_Contig/Conti...    36  0.021
Contig-U14174-1 (Contig-U14174-1Q) /CSM_Contig/Conti...    34  0.084

>Contig-U13388-1 (Contig-U13388-1Q) /CSM_Contig/Contig-U13388-1Q.Seq.d
          Length = 312

 Score =  268 bits (135), Expect = 3e-72
 Identities = 135/135 (100%)
 Strand = Plus / Plus

                                                                       
Query: 178 ccaccaatttggccagcaccgttctatggtcaatttggtaataattcaatattaatttca 237
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 178 ccaccaatttggccagcaccgttctatggtcaatttggtaataattcaatattaatttca 237

                                                                       
Query: 238 aaagaatttaattttacaataatatctgattcaacattattattaaataaaactttatca 297
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 238 aaagaatttaattttacaataatatctgattcaacattattattaaataaaactttatca 297

                          
Query: 298 aaatattataattta 312
           |||||||||||||||
Sbjct: 298 aaatattataattta 312


 Score =  101 bits (51), Expect = 4e-22
 Identities = 65/72 (90%)
 Strand = Plus / Plus

                                                                       
Query: 44  tgataattttaaaaaggaatatagnnnnnnnacttataataattattgttttaggtatat 103
           ||||||||||||||||||||||||       |||||||||||||||||||||||||||||
Sbjct: 44  tgataattttaaaaaggaatatagtttttttacttataataattattgttttaggtatat 103

                       
Query: 104 ttatagcaacat 115
           ||||||||||||
Sbjct: 104 ttatagcaacat 115


 Score = 34.2 bits (17), Expect = 0.084
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                           
Query: 1  caccaatctttataatt 17
          |||||||||||||||||
Sbjct: 1  caccaatctttataatt 17


>Contig-U10839-1 (Contig-U10839-1Q) /CSM_Contig/Contig-U10839-1Q.Seq.d
          Length = 3083

 Score = 38.2 bits (19), Expect = 0.005
 Identities = 19/19 (100%)
 Strand = Plus / Minus

                               
Query: 283  aataaaactttatcaaaat 301
            |||||||||||||||||||
Sbjct: 2347 aataaaactttatcaaaat 2329


 Score = 30.2 bits (15), Expect = 1.3
 Identities = 18/19 (94%)
 Strand = Plus / Minus

                               
Query: 283  aataaaactttatcaaaat 301
            |||||||||||||| ||||
Sbjct: 1242 aataaaactttatctaaat 1224


>Contig-U14478-1 (Contig-U14478-1Q) /CSM_Contig/Contig-U14478-1Q.Seq.d
          Length = 152

 Score = 36.2 bits (18), Expect = 0.021
 Identities = 21/22 (95%)
 Strand = Plus / Plus

                                 
Query: 225 aatattaatttcaaaagaattt 246
           |||||||||||||| |||||||
Sbjct: 71  aatattaatttcaatagaattt 92


  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: 9238
Number of Sequences: 6905
Number of extensions: 9238
Number of successful extensions: 1106
Number of sequences better than 10.0: 358
length of query: 312
length of database: 5,674,871
effective HSP length: 15
effective length of query: 297
effective length of database: 5,571,296
effective search space: 1654674912
effective search space used: 1654674912
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. 9
Homology vs DNA 
Query= Contig-U13388-1 (Contig-U13388-1Q) /CSM_Contig/Contig-U13388-1Q.Seq.d
         (312 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

(AU071489) Dictyostelium discoideum slug cDNA, clone SSB640.      125   7e-55  4
(X95275) Plasmodium falciparum complete gene map of plastid-...    36   7e-04  5
(AF250284) Amsacta moorei entomopoxvirus, complete genome.         40   0.002  6
(AE017263) Mesoplasma florum L1 complete genome.                   40   0.004  8
(DQ642846) Plasmodium falciparum HB3 apicoplast, complete ge...    36   0.007  5
(AE014841) Plasmodium falciparum 3D7 chromosome 11 section 6...    42   0.009  6
(AC120107) Rattus norvegicus chromosome 1 clone RP32-274G9 m...    52   0.012  1
(AC112825) Rattus norvegicus clone CH230-20P5, WORKING DRAFT...    52   0.012  1
(AC106322) Rattus norvegicus clone CH230-185B24, WORKING DRA...    52   0.012  1
(EJ687297) 1092955195251 Global-Ocean-Sampling_GS-30-02-01-1...    50   0.046  1
(EJ399430) 1093012026174 Global-Ocean-Sampling_GS-28-01-01-1...    50   0.046  1
(AC176331) Strongylocentrotus purpuratus clone R3-3053I3, WO...    38   0.046  4
(AJ294725) Astasia longa complete chloroplast genome.              34   0.060  6
(AL049184) Plasmodium falciparum DNA *** SEQUENCING IN PROGR...    34   0.068  10
(AC153449) Bos taurus clone CH240-20F8, WORKING DRAFT SEQUEN...    40   0.076  3
(AL731896) Mouse DNA sequence from clone RP23-348D11 on chro...    38   0.16   5
(CL869962) abe58f09.x1 Soybean methylation filtered genomic ...    32   0.17   3
(AC144420) Rattus norvegicus clone CH230-481A14, *** SEQUENC...    48   0.18   1
(BZ051416) jnr60h07.b1 B.oleracea001 Brassica oleracea genom...    48   0.18   1
(CU367882) H.melpomene DNA sequence from clone AEHM-11J7.          40   0.24   4
(AC116986) Dictyostelium discoideum chromosome 2 map 2234041...    32   0.26   10
(CP000768) Campylobacter jejuni subsp. doylei 269.97, comple...    32   0.35   2
(AP009180) Candidatus Carsonella ruddii PV DNA, complete gen...    30   0.36   8
(BX004770) Zebrafish DNA sequence from clone DKEY-14K21 in l...    32   0.39   2
(BX120000) Zebrafish DNA sequence from clone CH211-214C13 in...    34   0.40   2
(AC116963) Dictyostelium discoideum chromosome 2 map 4657875...    38   0.41   4
(AC201457) Strongylocentrotus purpuratus clone R3-3037H20, W...    40   0.47   2
(AY816330) Campylobacter jejuni subsp. doylei strain RM2095 ...    32   0.48   2
(AF538053) Monosiga brevicollis mitochondrion, complete genome.    32   0.49   5
(EK412961) 1095505211303 Global-Ocean-Sampling_GS-31-01-01-1...    34   0.52   2
(EJ589740) 1092961042117 Global-Ocean-Sampling_GS-29-01-01-1...    32   0.52   2
(AC116984) Dictyostelium discoideum chromosome 2 map 2567470...    34   0.53   11
(AC174277) Medicago truncatula clone mth2-5i22, complete seq...    42   0.53   4
(BI581545) RH19046.5prime RH Drosophila melanogaster normali...    38   0.57   2
(AC009323) Arabidopsis thaliana chromosome I BAC F25P12 geno...    46   0.72   1
(AC197976) Myotis lucifugus clone CH235-61N22, WORKING DRAFT...    46   0.72   1
(ED261818) AUAC-aaf35f04.g1 Ascaris suum whole genome shotgu...    46   0.72   1
(DX897670) KBrH028L14R KBrH, Brassica rapa HindIII BAC libra...    46   0.72   1
(DX891132) KBrH019B19R KBrH, Brassica rapa HindIII BAC libra...    46   0.72   1
(CT017754) KBrH129B19 genomic clone, KBrH (HindIII) BAC libr...    46   0.72   1
(CT016990) KBrH128B19 genomic clone, KBrH (HindIII) BAC libr...    46   0.72   1
(DU883618) 392351 Tomato HindIII BAC Library Solanum lycoper...    36   0.79   2
(AC117075) Dictyostelium discoideum chromosome 2 map 5201047...    36   0.84   6
(AX392733) Sequence 23 from Patent WO0212526.                      40   0.86   4
(AR707080) Sequence 23 from patent US 6933145.                     40   0.86   4
(AC179164) Strongylocentrotus purpuratus clone R3-4016E3, WO...    36   0.89   3
(AC152746) Bos taurus clone CH240-7D8, WORKING DRAFT SEQUENC...    40   0.90   4
(AY573124) Otites centralis 16S ribosomal RNA gene, partial ...    40   1.1    2
(CF945677) TrEST-A0770 TrEST-A Hypocrea jecorina cDNA clone ...    42   1.2    2
(AC094933) Rattus norvegicus clone CH230-6D20, *** SEQUENCIN...    34   1.4    2
(AC097394) Rattus norvegicus clone CH230-10B1, *** SEQUENCIN...    34   1.4    2
(AP007964) Lotus japonicus genomic DNA, chromosome 4, clone:...    40   1.4    4
(AC128993) Rattus norvegicus clone CH230-1L11, *** SEQUENCIN...    34   1.4    2
(AC142035) Rattus norvegicus clone CH230-262A11, WORKING DRA...    34   1.5    2
(AF000948) Borrelia burgdorferi oligopeptide permease homolo...    32   1.5    4
(CT030144) Zebrafish DNA sequence from clone CH73-367J5 in l...    32   1.5    2
(EK570273) 1095521073400 Global-Ocean-Sampling_GS-32-01-01-1...    34   1.7    3
(CP000263) Buchnera aphidicola str. Cc (Cinara cedri), compl...    32   1.7    9
(AX347207) Sequence 2278 from Patent WO0200928.                    34   1.7    4
(Z98551) Plasmodium falciparum MAL3P6.                             38   1.8    5
(AC204582) Zea mays chromosome 6 clone CH201-319L2; ZMMBBc03...    42   1.8    2
(AF404306) Rhizophydium sp. 136 mitochondrion, complete genome.    34   1.9    4
(AC214043) Zea mays chromosome 5 clone CH201-299G22; ZMMBBc0...    42   1.9    2
(BX465834) Zebrafish DNA sequence from clone CH211-202E12 in...    38   1.9    2
(AY456189) Hutchinsoniella macracantha mitochondrion, comple...    32   2.0    4
(ER859469) PPTHK17TF Solanum tuberosum RHPOTKEY BAC ends Sol...    36   2.0    2
(AC202324) Medicago truncatula clone mth2-160m22, WORKING DR...    38   2.1    5
(AE014826) Plasmodium falciparum 3D7 chromosome 14 section 1...    36   2.1    5
(AC231890) Lama pacos clone CH246-336C5, WORKING DRAFT SEQUE...    38   2.2    2
(AL162373) Human DNA sequence from clone RP11-272M24 on chro...    40   2.2    5
(AL929355) Plasmodium falciparum strain 3D7, chromosome 9; s...    34   2.3    6
(DQ927305) Tetrahymena pigmentosa strain UM1060 mitochondrio...    32   2.4    4
(ER800570) PPTID84TR Solanum tuberosum RHPOTKEY BAC ends Sol...    36   2.5    2
(ED742942) GM_WBb0105L05.r GM_WBb Glycine max genomic clone ...    40   2.6    2
(ED166338) AUAC-aay70b05.b1 Ascaris suum whole genome shotgu...    34   2.6    2
(EJ964037) 1093022027502 Global-Ocean-Sampling_GS-30-02-01-1...    40   2.7    2
(ET899003) CHO_OF145xk02r1.ab1 CHO_OF Nicotiana tabacum geno...    38   2.8    2
(FI069847) CHO_OF7312xb12r1.ab1 CHO_OF7 Nicotiana tabacum ge...    38   2.8    2
(CU469461) Zebrafish DNA sequence from clone CH73-50K9 in li...    44   2.8    1
(BX537309) Zebrafish DNA sequence from clone CH211-225N7 in ...    44   2.8    1
(BV266399) S235P6322FG5.T0 ItalianGreyhound Canis familiaris...    44   2.8    1
(AL844603) Mouse DNA sequence from clone RP24-334I20 on chro...    44   2.8    1
(AC107456) Mus musculus chromosome 3, clone RP23-273L6, comp...    44   2.8    1
(AP008208) Oryza sativa (japonica cultivar-group) genomic DN...    44   2.8    1
(AP005885) Oryza sativa Japonica Group genomic DNA, chromoso...    44   2.8    1
(GC513648) Sequence 1996 from patent US 7405291.                   44   2.8    1
(GC508912) Sequence 1996 from patent US 7404958.                   44   2.8    1
(GC496400) Sequence 1996 from patent US 7396532.                   44   2.8    1
(GC486530) Sequence 1996 from patent US 7390493.                   44   2.8    1
(GC483311) Sequence 1996 from patent US 7388090.                   44   2.8    1
(GC478358) Sequence 1996 from patent US 7385047.                   44   2.8    1
(EA779487) Sequence 1996 from patent US 7381816.                   44   2.8    1
(EA776824) Sequence 1996 from patent US 7381815.                   44   2.8    1
(EA774161) Sequence 1996 from patent US 7381814.                   44   2.8    1
(EA768537) Sequence 1996 from patent US 7378514.                   44   2.8    1
(EA763544) Sequence 1996 from patent US 7378258.                   44   2.8    1
(EA445169) Sequence 1996 from patent US 7338786.                   44   2.8    1
(EA438512) Sequence 1996 from patent US 7335494.                   44   2.8    1
(EA435849) Sequence 1996 from patent US 7335493.                   44   2.8    1
(EA422437) Sequence 1996 from patent US 7326544.                   44   2.8    1

>(AU071489) Dictyostelium discoideum slug cDNA, clone SSB640.
          Length = 240

 Score =  125 bits (63), Expect(4) = 7e-55
 Identities = 63/63 (100%)
 Strand = Plus / Plus


Query: 178 ccaccaatttggccagcaccgttctatggtcaatttggtaataattcaatattaatttca 237
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 178 ccaccaatttggccagcaccgttctatggtcaatttggtaataattcaatattaatttca 237


Query: 238 aaa 240
           |||
Sbjct: 238 aaa 240

 Score = 79.8 bits (40), Expect(4) = 7e-55
 Identities = 40/40 (100%)
 Strand = Plus / Plus


Query: 75  acttataataattattgttttaggtatatttatagcaaca 114
           ||||||||||||||||||||||||||||||||||||||||
Sbjct: 75  acttataataattattgttttaggtatatttatagcaaca 114

 Score = 48.1 bits (24), Expect(4) = 7e-55
 Identities = 24/24 (100%)
 Strand = Plus / Plus


Query: 44 tgataattttaaaaaggaatatag 67
          ||||||||||||||||||||||||
Sbjct: 44 tgataattttaaaaaggaatatag 67

 Score = 34.2 bits (17), Expect(4) = 7e-55
 Identities = 17/17 (100%)
 Strand = Plus / Plus


Query: 1  caccaatctttataatt 17
          |||||||||||||||||
Sbjct: 1  caccaatctttataatt 17

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 354,387,370
Number of extensions: 26246236
Number of successful extensions: 2460797
Number of sequences better than 10.0: 243
Length of query: 312
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 289
Effective length of database: 93,106,754,628
Effective search space: 26907852087492
Effective search space used: 26907852087492
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 7
Homology vs Protein 
Query= Contig-U13388-1 (Contig-U13388-1Q) /CSM_Contig/Contig-U13388-1Q.Seq.d
         (312 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54K55) RecName: Full=Beta-hexosaminidase subunit B1;          ...   147   1e-34
(Q54K56) RecName: Full=Beta-hexosaminidase subunit B2;          ...    33   2.4
AF295546_3(AF295546|pid:none) Malawimonas jakobiformis mitochond...    33   4.1

>(Q54K55) RecName: Full=Beta-hexosaminidase subunit B1;
           EC=3.2.1.52; AltName: Full=N-acetyl-beta-glucosaminidase
           subunit B1; AltName: Full=Beta-N-acetylhexosaminidase
           subunit B1; Flags: Precursor;
          Length = 560

 Score =  147 bits (371), Expect = 1e-34
 Identities = 75/90 (83%), Positives = 75/90 (83%)
 Frame = +1

Query: 43  MIILKRNXXXXXXXXXXXXXXXATSIEIKNYKLSLNQNKNEISKNPPIWPAPFYGQFGNN 222
           MIILKRN               ATSIEIKNYKLSLNQNKNEISKNPPIWPAPFYGQFGNN
Sbjct: 1   MIILKRNIVFLLIIIIVLGIFIATSIEIKNYKLSLNQNKNEISKNPPIWPAPFYGQFGNN 60

Query: 223 SILISKEFNFTIISDSTLLLNKTLSKYYNL 312
           SILISKEFNFTIISDSTLLLNKTLSKYYNL
Sbjct: 61  SILISKEFNFTIISDSTLLLNKTLSKYYNL 90

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: 300,107,499
Number of extensions: 4549846
Number of successful extensions: 10387
Number of sequences better than 10.0: 3
Number of HSP's gapped: 10385
Number of HSP's successfully gapped: 3
Length of query: 104
Length of database: 1,051,180,864
Length adjustment: 72
Effective length of query: 32
Effective length of database: 818,148,616
Effective search space: 26180755712
Effective search space used: 26180755712
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: 28 (15.4 bits)
PSORT 

 psg: 0.65  gvh: 0.54  alm: 0.07  top: -0.13  tms: 0.07  mit: 0.33  mip: 0.04
 nuc: 0.20  erl: 0.00  erm: 0.20  pox: 0.00  px2: 0.00  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 1.00  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 : 1.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 0.00 

	 24.0 %: cytoplasmic
	 24.0 %: mitochondrial
	 16.0 %: nuclear
	 12.0 %: Golgi
	 12.0 %: endoplasmic reticulum
	  4.0 %: extracellular, including cell wall
	  4.0 %: vacuolar
	  4.0 %: peroxisomal

>> prediction for Contig-U13388-1 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