Contig-U13720-1
Contig ID Contig-U13720-1
Contig update 2002.12.18
Contig sequence
>Contig-U13720-1 (Contig-U13720-1Q) /CSM_Contig/Contig-U13720-1Q.Seq.d
AAACAAGAGTCGGAACAACGTAAAAAACAATATGAAGATCATTTGAAAGA
AAGAGAATCAGAGAGAGAGAAAGAGGTTCAACAATTATTATTAAAACAAA
AAGAAGCTGAACAATTAATTGAACAACAAAAACAAGATCAACAAAAGCTC
AAACAAGAGAGAGAACTTGAAATTCGTAAACAACAACAATTGGAACACCA
ATTGGAAGAGGAGAGAAAACAAGAACAAAAGAAAAAGAAAGAATTGGATG
ATCAAGAATGGAAGAGAAAGGAACAACAATATCAATCTGATCCTCAATTA
GAAAAAGAAGAAAGAGAAAGAAATGAGAAACTTGAAAAAGATAGACAATT
ACAATTAGAACAAGAAATTGAAAAAGAAAGAAAATTAAAACAACAACAAA
AAGAAAAAGAACAAAAAGAACAAAAAGAAAAAAGAGAACAAAGAGAAAAA
GAAGAAAAAGAAGAAAAAGATAAAAAAGATAAAGAAGAAAAAGAAAAACA
AGAATTAAAGAAAAAACAACAACAACAACAACAACAAAAAGAAAAAGAAN
NNNNNNNN

Gap no gap
Contig length 558
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 U13720
List of clone(s)

est1=VHK525F,1,549
Translated Amino Acid sequence
KQESEQRKKQYEDHLKERESEREKEVQQLLLKQKEAEQLIEQQKQDQQKLKQERELEIRK
QQQLEHQLEEERKQEQKKKKELDDQEWKRKEQQYQSDPQLEKEERERNEKLEKDRQLQLE
QEIEKERKLKQQQKEKEQKEQKEKREQREKEEKEEKDKKDKEEKEKQELKKKQQQQQQQK
EKEXXX


Translated Amino Acid sequence (All Frames)
Frame A:
KQESEQRKKQYEDHLKERESEREKEVQQLLLKQKEAEQLIEQQKQDQQKLKQERELEIRK
QQQLEHQLEEERKQEQKKKKELDDQEWKRKEQQYQSDPQLEKEERERNEKLEKDRQLQLE
QEIEKERKLKQQQKEKEQKEQKEKREQREKEEKEEKDKKDKEEKEKQELKKKQQQQQQQK
EKEXXX


Frame B:
nksrnnvknnmkii*kkenqrerkrfnnyy*nkkklnn*lnnknkinkssnkrenlkfvn
nnnwntnwkrrenknkrkrknwmikngrernnninliln*kkkkekemrnlkkidnyn*n
kklkkken*nnnkkkknkknkkkkenkekkkkkkkkikkikkkkknkn*rknnnnnnnkk
kkxxx


Frame C:
trvgtt*kti*rsferkrirerergstiiiktkrs*tin*ttktrstkaqtrert*ns*t
ttigtpigrgektrtkekerig*srmeekgttisi*ssirkrrkrkk*et*kr*titirt
rn*krkkiktttkrkrtkrtkrkkrtkrkrrkrrkr*kr*rrkrktrikektttttttkr
krxxx


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U13720-1 (Contig-U13720-1Q)
/CSM_Contig/Contig-U13720-1Q.Seq.d
(558 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U13720-1 (Contig-U13720-1Q) /CSM_Contig/Conti... 111 8e-25
Contig-U12300-1 (Contig-U12300-1Q) /CSM_Contig/Conti... 103 2e-22
Contig-U12528-1 (Contig-U12528-1Q) /CSM_Contig/Conti... 36 0.039
Contig-U13357-1 (Contig-U13357-1Q) /CSM_Contig/Conti... 34 0.15
Contig-U13980-1 (Contig-U13980-1Q) /CSM_Contig/Conti... 32 0.61
Contig-U13580-1 (Contig-U13580-1Q) /CSM_Contig/Conti... 32 0.61
Contig-U12830-1 (Contig-U12830-1Q) /CSM_Contig/Conti... 32 0.61
Contig-U12565-1 (Contig-U12565-1Q) /CSM_Contig/Conti... 32 0.61
Contig-U11845-1 (Contig-U11845-1Q) /CSM_Contig/Conti... 32 0.61
Contig-U11841-1 (Contig-U11841-1Q) /CSM_Contig/Conti... 32 0.61

>Contig-U13720-1 (Contig-U13720-1Q) /CSM_Contig/Contig-U13720-1Q.Seq.d
Length = 558

Score = 111 bits (56), Expect = 8e-25
Identities = 56/56 (100%)
Strand = Plus / Plus


Query: 244 ttggatgatcaagaatggaagagaaaggaacaacaatatcaatctgatcctcaatt 299
||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 244 ttggatgatcaagaatggaagagaaaggaacaacaatatcaatctgatcctcaatt 299


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


Query: 158 agagagaacttgaaattcgtaaacaacaacaattggaacaccaattg 204
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 158 agagagaacttgaaattcgtaaacaacaacaattggaacaccaattg 204


Score = 87.7 bits (44), Expect = 1e-17
Identities = 44/44 (100%)
Strand = Plus / Plus


Query: 1 aaacaagagtcggaacaacgtaaaaaacaatatgaagatcattt 44
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 aaacaagagtcggaacaacgtaaaaaacaatatgaagatcattt 44


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


Query: 76 gttcaacaattattattaaaa 96
|||||||||||||||||||||
Sbjct: 76 gttcaacaattattattaaaa 96


>Contig-U12300-1 (Contig-U12300-1Q) /CSM_Contig/Contig-U12300-1Q.Seq.d
Length = 3886

Score = 103 bits (52), Expect = 2e-22
Identities = 55/56 (98%)
Strand = Plus / Plus


Query: 244 ttggatgatcaagaatggaagagaaaggaacaacaatatcaatctgatcctcaatt 299
||||||||||||||||||||||||||||||||||||||||||||||||| ||||||
Sbjct: 735 ttggatgatcaagaatggaagagaaaggaacaacaatatcaatctgatcttcaatt 790


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


Query: 158 agagagaacttgaaattcgtaaacaacaacaattggaacaccaattg 204
|||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 649 agagagaacttgaaattcgtaaacaacaacaattggaacaccaattg 695


Score = 87.7 bits (44), Expect = 1e-17
Identities = 44/44 (100%)
Strand = Plus / Plus


Query: 1 aaacaagagtcggaacaacgtaaaaaacaatatgaagatcattt 44
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 492 aaacaagagtcggaacaacgtaaaaaacaatatgaagatcattt 535


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


Query: 76 gttcaacaattattattaaaa 96
|||||||||||||||||||||
Sbjct: 567 gttcaacaattattattaaaa 587


Score = 32.2 bits (16), Expect = 0.61
Identities = 16/16 (100%)
Strand = Plus / Plus


Query: 178 aaacaacaacaattgg 193
||||||||||||||||
Sbjct: 1504 aaacaacaacaattgg 1519


Score = 32.2 bits (16), Expect = 0.61
Identities = 19/20 (95%)
Strand = Plus / Plus


Query: 178 aaacaacaacaattggaaca 197
|||||||||||||| |||||
Sbjct: 3757 aaacaacaacaattagaaca 3776


Score = 28.2 bits (14), Expect = 9.5
Identities = 17/18 (94%)
Strand = Plus / Plus


Query: 180 acaacaacaattggaaca 197
||||||||||| ||||||
Sbjct: 923 acaacaacaatgggaaca 940


>Contig-U12528-1 (Contig-U12528-1Q) /CSM_Contig/Contig-U12528-1Q.Seq.d
Length = 1995

Score = 36.2 bits (18), Expect = 0.039
Identities = 24/26 (92%)
Strand = Plus / Plus


Query: 14 aacaacgtaaaaaacaatatgaagat 39
||||||||||| |||||||| |||||
Sbjct: 1861 aacaacgtaaacaacaatatcaagat 1886


Score = 28.2 bits (14), Expect = 9.5
Identities = 14/14 (100%)
Strand = Plus / Plus


Query: 272 aacaacaatatcaa 285
||||||||||||||
Sbjct: 1870 aacaacaatatcaa 1883


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: 10,240
Number of Sequences: 6905
Number of extensions: 10240
Number of successful extensions: 667
Number of sequences better than 10.0: 161
length of query: 558
length of database: 5,674,871
effective HSP length: 16
effective length of query: 542
effective length of database: 5,564,391
effective search space: 3015899922
effective search space used: 3015899922
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 2008.12.13
Homology vs DNA
Query= Contig-U13720-1 (Contig-U13720-1Q) /CSM_Contig/Contig-U13720-1Q.Seq.d
(558 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

(BJ424371) Dictyostelium discoideum cDNA clone:ddv52a07, 5' ... 88 6e-18 2
(BJ412432) Dictyostelium discoideum cDNA clone:ddv8n10, 5' e... 88 1e-15 2
(BJ423900) Dictyostelium discoideum cDNA clone:ddv50c24, 5' ... 88 1e-15 2
(BJ418024) Dictyostelium discoideum cDNA clone:ddv31l07, 5' ... 88 1e-15 2
(BJ440940) Dictyostelium discoideum cDNA clone:ddv45n03, 3' ... 88 1e-15 2
(BJ421826) Dictyostelium discoideum cDNA clone:ddv43p22, 5' ... 88 8e-14 2
(BJ440727) Dictyostelium discoideum cDNA clone:ddv44e18, 3' ... 88 4e-13 1
(BJ426608) Dictyostelium discoideum cDNA clone:ddv59h17, 5' ... 88 4e-13 1
(BJ421006) Dictyostelium discoideum cDNA clone:ddv41k11, 5' ... 88 4e-13 1
(BJ419728) Dictyostelium discoideum cDNA clone:ddv37c02, 5' ... 88 4e-13 1
(BJ419674) Dictyostelium discoideum cDNA clone:ddv36h20, 5' ... 88 4e-13 1
(BJ425397) Dictyostelium discoideum cDNA clone:ddv55h15, 5' ... 58 4e-04 1

>(BJ424371) Dictyostelium discoideum cDNA clone:ddv52a07, 5' end,
single read.
Length = 549

Score = 87.7 bits (44), Expect(2) = 6e-18
Identities = 44/44 (100%)
Strand = Plus / Plus


Query: 1 aaacaagagtcggaacaacgtaaaaaacaatatgaagatcattt 44
||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 aaacaagagtcggaacaacgtaaaaaacaatatgaagatcattt 44

Score = 40.1 bits (20), Expect(2) = 6e-18
Identities = 20/20 (100%)
Strand = Plus / Plus


Query: 280 tatcaatctgatcctcaatt 299
||||||||||||||||||||
Sbjct: 280 tatcaatctgatcctcaatt 299

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 58,574,159
Number of extensions: 3162180
Number of successful extensions: 199090
Number of sequences better than 10.0: 12
Length of query: 558
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 535
Effective length of database: 93,106,754,628
Effective search space: 49812113725980
Effective search space used: 49812113725980
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)

protein update 2009. 7. 8
Homology vs Protein
Query= Contig-U13720-1 (Contig-U13720-1Q) /CSM_Contig/Contig-U13720-1Q.Seq.d
(558 letters)

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

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

***** No hits found ******

Lambda K H
0.299 0.118 0.304

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: 166,636,679
Number of extensions: 2040653
Number of successful extensions: 6120
Number of sequences better than 10.0: 0
Number of HSP's gapped: 6120
Number of HSP's successfully gapped: 0
Length of query: 186
Length of database: 1,051,180,864
Length adjustment: 121
Effective length of query: 65
Effective length of database: 659,557,225
Effective search space: 42871219625
Effective search space used: 42871219625
Neighboring words threshold: 12
Window for multiple hits: 40
X1: 16 ( 6.9 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (20.8 bits)
S2: 30 (16.2 bits)

PSORT

psg: 0.35 gvh: 0.25 alm: 0.70 top: 0.53 tms: 0.00 mit: 0.19 mip: 0.00
nuc: 0.29 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: 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

64.0 %: nuclear
20.0 %: cytoplasmic
8.0 %: mitochondrial
4.0 %: cytoskeletal
4.0 %: plasma membrane

>> prediction for Contig-U13720-1 is nuc

VS (DIR, S) 0
VH (FL, L) 1
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
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