Contig-U05297-1
Contig ID Contig-U05297-1
Contig update 2001. 8.29
Contig sequence
>Contig-U05297-1 (Contig-U05297-1Q) /CSM_Contig/Contig-U05297-1Q.Seq.d
AAAAAAAAAAAGAAAAAAAAAAAAGCAATAGTAAAATAAAAAAATCCTTA
TATTATAACTATTGTCAAAAAATTAAATAAATAAATTCAATGTAATAAAA
TAAAACTTAG

Gap no gap
Contig length 110
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 733899
End point 733789
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U05297
List of clone(s)

est1=SSG859E,1,111
Translated Amino Acid sequence
KKKEKKKSNSKIKKSLYYNYCQKIK*insm**nkt*


Translated Amino Acid sequence (All Frames)
Frame A:
kkkkkkkkaivk*knpyiitivkklnk*iqcnkikl


Frame B:
kkkrkkkkq**nkkilil*llskn*inkfnvik*nl


Frame C:
KKKEKKKSNSKIKKSLYYNYCQKIK*insm**nkt*


own update ----------
Homology vs CSM-cDNA -
dna update 2009. 7.18
Homology vs DNA
Query= Contig-U05297-1 (Contig-U05297-1Q) /CSM_Contig/Contig-U05297-1Q.Seq.d
(110 letters)

Database: ddbj_B
105,743,758 sequences; 104,622,809,269 total letters

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

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

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 105743758
Number of Hits to DB: 0
Number of sequences better than 10.0: 0
Length of query: 110
Length of database: 104,622,809,269
Length adjustment: 22
Effective length of query: 88
Effective length of database: 102,296,446,593
Effective search space: 9002087300184
Effective search space used: 9002087300184
X1: 11 (21.8 bits)
S2: 20 (40.1 bits)

protein update 2009. 8. 1
Homology vs Protein
Query= Contig-U05297-1 (Contig-U05297-1Q) /CSM_Contig/Contig-U05297-1Q.Seq.d
(110 letters)

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

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

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

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: 65,188,309
Number of extensions: 435386
Number of successful extensions: 278
Number of sequences better than 10.0: 0
Number of HSP's gapped: 278
Number of HSP's successfully gapped: 0
Length of query: 36
Length of database: 1,061,185,681
Length adjustment: 10
Effective length of query: 26
Effective length of database: 1,028,501,201
Effective search space: 26741031226
Effective search space used: 26741031226
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: 24 (13.9 bits)

PSORT

psg: 0.58 gvh: 0.01 alm: 0.76 top: 0.53 tms: 0.00 mit: 0.32 mip: 0.00
nuc: 0.37 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

72.0 %: nuclear
16.0 %: cytoplasmic
4.0 %: cytoskeletal
4.0 %: mitochondrial
4.0 %: plasma membrane

>> prediction for Contig-U05297-1 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