Contig-U01953-1
Contig ID Contig-U01953-1
Contig update 2001. 8.29
Contig sequence
>Contig-U01953-1 (Contig-U01953-1Q) /CSM_Contig/Contig-U01953-1Q.Seq.d
CTTTATCACAATTTTGACAATACAATTAACAACCAAAAATGGAAATTATT
AAACACAAAAAATGAAGGATTAAAAATAACATAAAGTATCCACTGTTAAT
ACACGGATTTTACACAATTTTTTAACAACTTTAAGGAACCCCCGGTGNTA
TTAAAAAAATACACAACAAAAAACCCATATTACAACCATTATAATTCCCC
AGGAAAAAACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAACCC
TAGAAAATATTTAAATTATTCAAATAAAAAAACAATTATAAAATATTTTA
AAAAAAT

Gap no gap
Contig length 307
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 U01953
List of clone(s)

est1=SSL670Z,1,308
Translated Amino Acid sequence
lyhnfdntinnqkwkllntkneglkit*sihc*YTDFTQFFNNFKEPPVXLKKYTTKNPY
YNHYNSPGKNKKKKKKKKKKKQTLENI*iiqikkql*nilkk


Translated Amino Acid sequence (All Frames)
Frame A:
lyhnfdntinnqkwkllntkneglkit*sihc*YTDFTQFFNNFKEPPVXLKKYTTKNPY
YNHYNSPGKNKKKKKKKKKKKQTLENI*iiqikkql*nilkk


Frame B:
fitiltiqlttkngny*tqkmkd*k*hkvstvntrilhnflttlrnprxy*kntqqkthi
ttiiipqektkkkkkkkkkknkp*kifklfk*knnykif*kn


Frame C:
lsqf*qyn*qpkmeiikhkk*riknnikypllihgfytif*ql*gtpgxikkihnkkpil
qpl*fprkkqkkkkkkkkkktnprkylnysnkktiikyfkk


own update 2004. 6. 9
Homology vs CSM-cDNA
Query= Contig-U01953-1 (Contig-U01953-1Q)
/CSM_Contig/Contig-U01953-1Q.Seq.d
(307 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U01953-1 (Contig-U01953-1Q) /CSM_Contig/Conti... 186 9e-48
Contig-U01404-1 (Contig-U01404-1Q) /CSM_Contig/Conti... 34 0.083
Contig-U11792-1 (Contig-U11792-1Q) /CSM_Contig/Conti... 32 0.33
Contig-U09459-1 (Contig-U09459-1Q) /CSM_Contig/Conti... 32 0.33
Contig-U06209-1 (Contig-U06209-1Q) /CSM_Contig/Conti... 32 0.33
Contig-U13855-1 (Contig-U13855-1Q) /CSM_Contig/Conti... 30 1.3
Contig-U10800-1 (Contig-U10800-1Q) /CSM_Contig/Conti... 30 1.3
Contig-U09778-1 (Contig-U09778-1Q) /CSM_Contig/Conti... 30 1.3
Contig-U07284-1 (Contig-U07284-1Q) /CSM_Contig/Conti... 30 1.3
Contig-U05022-1 (Contig-U05022-1Q) /CSM_Contig/Conti... 30 1.3

>Contig-U01953-1 (Contig-U01953-1Q) /CSM_Contig/Contig-U01953-1Q.Seq.d
Length = 307

Score = 186 bits (94), Expect = 9e-48
Identities = 111/118 (94%)
Strand = Plus / Plus


Query: 86 gtatccactgttaatacacggattttacacaattttttaacaactttaaggaacccccgg 145
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86 gtatccactgttaatacacggattttacacaattttttaacaactttaaggaacccccgg 145


Query: 146 tgntattnnnnnnntacacaacaaaaaacccatattacaaccattataattccccagg 203
||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 146 tgntattaaaaaaatacacaacaaaaaacccatattacaaccattataattccccagg 203


Score = 63.9 bits (32), Expect = 9e-11
Identities = 32/32 (100%)
Strand = Plus / Plus


Query: 1 ctttatcacaattttgacaatacaattaacaa 32
||||||||||||||||||||||||||||||||
Sbjct: 1 ctttatcacaattttgacaatacaattaacaa 32


>Contig-U01404-1 (Contig-U01404-1Q) /CSM_Contig/Contig-U01404-1Q.Seq.d
Length = 108

Score = 34.2 bits (17), Expect = 0.083
Identities = 17/17 (100%)
Strand = Plus / Minus


Query: 117 attttttaacaacttta 133
|||||||||||||||||
Sbjct: 68 attttttaacaacttta 52


>Contig-U11792-1 (Contig-U11792-1Q) /CSM_Contig/Contig-U11792-1Q.Seq.d
Length = 1729

Score = 32.2 bits (16), Expect = 0.33
Identities = 16/16 (100%)
Strand = Plus / Plus


Query: 120 ttttaacaactttaag 135
||||||||||||||||
Sbjct: 793 ttttaacaactttaag 808


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: 1186
Number of Sequences: 6905
Number of extensions: 1186
Number of successful extensions: 341
Number of sequences better than 10.0: 36
length of query: 307
length of database: 5,674,871
effective HSP length: 15
effective length of query: 292
effective length of database: 5,571,296
effective search space: 1626818432
effective search space used: 1626818432
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. 5.10
Homology vs DNA
Query= Contig-U01953-1 (Contig-U01953-1Q) /CSM_Contig/Contig-U01953-1Q.Seq.d
(307 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

(C93744) Dictyostelium discoideum slug cDNA, clone SSL670. 127 4e-28 2
(EB250252) PEG003-C-032882-501 Normalized Pedal-Pleural Gang... 46 0.76 1
(EB239380) PEG003-C-225374-501 Normalized Pedal-Pleural Gang... 46 0.76 1
(GD240729) G1045P345FH10.T1 Aplysia californica Pooled Norma... 46 0.76 1
(GD212654) G1045P388FM12.T1 Aplysia californica Pooled Norma... 46 0.76 1
(EK171993) 1095458079323 Global-Ocean-Sampling_GS-31-01-01-1... 32 2.0 2
(AC162142) Loxodonta africana clone VMRC15-510H22, WORKING D... 44 3.0 1
(AL591126) Mouse DNA sequence from clone RP23-188A3 on chrom... 42 7.7 2

>(C93744) Dictyostelium discoideum slug cDNA, clone SSL670.
Length = 308

Score = 127 bits (64), Expect(2) = 4e-28
Identities = 67/67 (100%)
Strand = Plus / Plus


Query: 86 gtatccactgttaatacacggattttacacaattttttaacaactttaaggaacccccgg 145
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 86 gtatccactgttaatacacggattttacacaattttttaacaactttaaggaacccccgg 145


Query: 146 tgntatt 152
|||||||
Sbjct: 146 tgntatt 152

Score = 32.2 bits (16), Expect(2) = 4e-28
Identities = 16/16 (100%)
Strand = Plus / Plus


Query: 1 ctttatcacaattttg 16
||||||||||||||||
Sbjct: 1 ctttatcacaattttg 16

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 83,736,248
Number of extensions: 4372616
Number of successful extensions: 321335
Number of sequences better than 10.0: 8
Length of query: 307
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 284
Effective length of database: 99,442,330,388
Effective search space: 28241621830192
Effective search space used: 28241621830192
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.18
Homology vs Protein
Query= Contig-U01953-1 (Contig-U01953-1Q) /CSM_Contig/Contig-U01953-1Q.Seq.d
(307 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

AE014187_149(AE014187|pid:none) Plasmodium falciparum 3D7 chromo... 32 5.4

>AE014187_149(AE014187|pid:none) Plasmodium falciparum 3D7
chromosome 14, complete sequence.
&AE014818_29(AE014818|pid:none)
Length = 1474

Score = 32.3 bits (72), Expect = 5.4
Identities = 20/68 (29%), Positives = 29/68 (42%), Gaps = 4/68 (5%)
Frame = +1

Query: 4 YHNFDNTINNQKWKLLNTKNEGLKIT*SIHC*YTDFTQFFNNFKEPPVXLK----KYTTK 171
YHN++N NN K+ + K + K D+ + N+KE K K+
Sbjct: 218 YHNYNNNNNNNKFYVSKNKYDNNK--------KNDYNFSYKNYKERYYYDKGNRIKHNNS 269

Query: 172 NPYYNHYN 195
YY HYN
Sbjct: 270 ITYYKHYN 277

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: 364,416,200
Number of extensions: 5593400
Number of successful extensions: 9541
Number of sequences better than 10.0: 1
Number of HSP's gapped: 9538
Number of HSP's successfully gapped: 1
Length of query: 102
Length of database: 1,051,180,864
Length adjustment: 70
Effective length of query: 32
Effective length of database: 824,621,734
Effective search space: 26387895488
Effective search space used: 26387895488
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: 0.75 gvh: 0.12 alm: 0.67 top: 0.53 tms: 0.00 mit: 0.20 mip: 0.00
nuc: 0.49 erl: 0.00 erm: 0.00 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

88.0 %: nuclear
4.0 %: cytoskeletal
4.0 %: plasma membrane
4.0 %: cytoplasmic

>> prediction for Contig-U01953-1 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