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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-U10493-1
Contig ID Contig-U10493-1
Contig update 2002. 9.13
Contig sequence 
>Contig-U10493-1 (Contig-U10493-1Q) /CSM_Contig/Contig-U10493-1Q.Seq.d
NNNNNNNNNNTCCCNNNNCGNTTCNTTGNNCNAGCNTTTNCNTNTTTNNC
AGCNTACNTCCGNTGGGTCGGNCCTGNATATAATGNAAAAATAATTCCNA
GNCNTTTATCNAGNATTCNAAATCCCATTTTTAGNTCCTTTGNNCNTAAG
GCTATNAACCCAGNGNCNATTCNAAAATATAAAACCCCAGNTGGGAATTT
CNGNTTAGATGAAGNGGNTTCNGNTTTCNAATCAGATTTNAACNCCCNTT
CNAATTTNTTAGGGTCNAAAACNTTTATTTTTGGNGGCCCTTTATCNATG
GCNGATATCNCCTTATTTTCNNCCTTGGCNCCAATTTNTTATG
Gap no gap
Contig length 343
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 U10493
List of clone(s) 

est1=VFM373Z,1,334
Translated Amino Acid sequence 
XXXXPXRFXXXAFXXXXAYXRWVGPXYNXKIIPXXLSXIXNPIFXSFXXKAXNPXXIXKY
KTPXGNFXLDEXXSXFXSDXNXXSNXLGSKTFIFGGPLSMADIXLFSXLAPIXY
Translated Amino Acid sequence (All Frames) 
Frame A:
XXXXPXRFXXXAFXXXXAYXRWVGPXYNXKIIPXXLSXIXNPIFXSFXXKAXNPXXIXKY
KTPXGNFXLDEXXSXFXSDXNXXSNXLGSKTFIFGGPLSMADIXLFSXLAPIXY


Frame B:
xxxsxxxslxxxxxxxqxtsxgsxlximxk*fxxxyxxfxipflxplxxrlxtqxxfxni
kpqxgisx*mkxxxxsnqixtpxxix*gxkxlflxalyxwxispyfxpwxqfxm


Frame C:
xxxpxxxxxxsxxxfxsxxpxgrxxi*xknnsxxfixxskshf*xlxx*gyxpxxxski*
npxwefxxr*xgfxfxirfxxpfxfxrvxnxyfwxpfixgxyxlifxlgxnxl
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U10493-1 (Contig-U10493-1Q)
/CSM_Contig/Contig-U10493-1Q.Seq.d
         (343 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U10493-1 (Contig-U10493-1Q) /CSM_Contig/Conti...   321  3e-88
Contig-U05912-1 (Contig-U05912-1Q) /CSM_Contig/Conti...   218  3e-57

>Contig-U10493-1 (Contig-U10493-1Q) /CSM_Contig/Contig-U10493-1Q.Seq.d
          Length = 343

 Score =  321 bits (162), Expect = 3e-88
 Identities = 294/294 (100%)
 Strand = Plus / Plus

                                                                       
Query: 50  cagcntacntccgntgggtcggncctgnatataatgnaaaaataattccnagncntttat 109
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 50  cagcntacntccgntgggtcggncctgnatataatgnaaaaataattccnagncntttat 109

                                                                       
Query: 110 cnagnattcnaaatcccatttttagntcctttgnncntaaggctatnaacccagngncna 169
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 110 cnagnattcnaaatcccatttttagntcctttgnncntaaggctatnaacccagngncna 169

                                                                       
Query: 170 ttcnaaaatataaaaccccagntgggaatttcngnttagatgaagnggnttcngntttcn 229
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 170 ttcnaaaatataaaaccccagntgggaatttcngnttagatgaagnggnttcngntttcn 229

                                                                       
Query: 230 aatcagatttnaacncccnttcnaatttnttagggtcnaaaacntttatttttggnggcc 289
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 230 aatcagatttnaacncccnttcnaatttnttagggtcnaaaacntttatttttggnggcc 289

                                                                 
Query: 290 ctttatcnatggcngatatcnccttattttcnnccttggcnccaatttnttatg 343
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 290 ctttatcnatggcngatatcnccttattttcnnccttggcnccaatttnttatg 343


>Contig-U05912-1 (Contig-U05912-1Q) /CSM_Contig/Contig-U05912-1Q.Seq.d
          Length = 1053

 Score =  218 bits (110), Expect = 3e-57
 Identities = 237/294 (80%)
 Strand = Plus / Plus

                                                                       
Query: 50  cagcntacntccgntgggtcggncctgnatataatgnaaaaataattccnagncntttat 109
           |||| ||| |||| |||||||  |||| |||||||| |||||||||||| || | |||||
Sbjct: 549 cagcatacatccgttgggtcgtacctgaatataatgaaaaaataattccaagacttttat 608

                                                                       
Query: 110 cnagnattcnaaatcccatttttagntcctttgnncntaaggctatnaacccagngncna 169
           | || |||| |||||| |||||||| || ||||  | ||||||||| |||| || | | |
Sbjct: 609 caagtattcaaaatccaatttttagatcatttgctcataaggctataaaccaagtgtcaa 668

                                                                       
Query: 170 ttcnaaaatataaaaccccagntgggaatttcngnttagatgaagnggnttcngntttcn 229
           ||| |||||||||||||| || ||| |||||| | |||||||||| || ||| | |||| 
Sbjct: 669 ttcaaaaatataaaacccaagttggtaatttcagtttagatgaagtggtttcagttttca 728

                                                                       
Query: 230 aatcagatttnaacncccnttcnaatttnttagggtcnaaaacntttatttttggnggcc 289
           |||||||||| ||| | | ||| ||||| ||||| || ||||| ||||||||||| | ||
Sbjct: 729 aatcagatttaaactcactttcaaatttattaggttcaaaaacttttatttttggtgacc 788

                                                                 
Query: 290 ctttatcnatggcngatatcnccttattttcnnccttggcnccaatttnttatg 343
            |||||| ||||| |||||| | ||||||||  | ||||| | ||||| |||||
Sbjct: 789 atttatcaatggcagatatctcattattttcaacattggctcaaatttattatg 842


  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: 627
Number of Sequences: 6905
Number of extensions: 627
Number of successful extensions: 11
Number of sequences better than 10.0: 3
length of query: 343
length of database: 5,674,871
effective HSP length: 15
effective length of query: 328
effective length of database: 5,571,296
effective search space: 1827385088
effective search space used: 1827385088
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 2008.11.20
Homology vs DNA 
Query= Contig-U10493-1 (Contig-U10493-1Q) /CSM_Contig/Contig-U10493-1Q.Seq.d
         (343 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

(BJ435002) Dictyostelium discoideum cDNA clone:ddv25b19, 3' ...   321   9e-84  1
(AC116987) Dictyostelium discoideum chromosome 2 map 3527441...   218   1e-52  1
(AU266482) Dictyostelium discoideum vegetative cDNA clone:VS...   204   1e-48  1
(C93160) Dictyostelium discoideum slug cDNA, clone SSM696.        200   2e-47  1
(AU268126) Dictyostelium discoideum vegetative cDNA clone:VS...   188   9e-44  1

>(BJ435002) Dictyostelium discoideum cDNA clone:ddv25b19, 3' end,
           single read.
          Length = 334

 Score =  321 bits (162), Expect = 9e-84
 Identities = 294/294 (100%)
 Strand = Plus / Minus


Query: 50  cagcntacntccgntgggtcggncctgnatataatgnaaaaataattccnagncntttat 109
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 295 cagcntacntccgntgggtcggncctgnatataatgnaaaaataattccnagncntttat 236


Query: 110 cnagnattcnaaatcccatttttagntcctttgnncntaaggctatnaacccagngncna 169
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 235 cnagnattcnaaatcccatttttagntcctttgnncntaaggctatnaacccagngncna 176


Query: 170 ttcnaaaatataaaaccccagntgggaatttcngnttagatgaagnggnttcngntttcn 229
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 175 ttcnaaaatataaaaccccagntgggaatttcngnttagatgaagnggnttcngntttcn 116


Query: 230 aatcagatttnaacncccnttcnaatttnttagggtcnaaaacntttatttttggnggcc 289
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 115 aatcagatttnaacncccnttcnaatttnttagggtcnaaaacntttatttttggnggcc 56


Query: 290 ctttatcnatggcngatatcnccttattttcnnccttggcnccaatttnttatg 343
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 55  ctttatcnatggcngatatcnccttattttcnnccttggcnccaatttnttatg 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 100,641,375
Number of extensions: 5558920
Number of successful extensions: 116205
Number of sequences better than 10.0: 5
Length of query: 343
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 320
Effective length of database: 93,106,754,628
Effective search space: 29794161480960
Effective search space used: 29794161480960
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 6.28
Homology vs Protein 
Query= Contig-U10493-1 (Contig-U10493-1Q) /CSM_Contig/Contig-U10493-1Q.Seq.d
         (343 letters)

Database: nrp_A
           3,204,285 sequences; 1,040,966,779 total letters

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AC116987_6(AC116987|pid:none) Dictyostelium discoideum chromosom...   124   1e-27
AY728062_1(AY728062|pid:none) Caenorhabditis elegans cadmium-ind...    33   2.4
T20215(T20215)hypothetical protein C54D10.2 - Caenorhabditis ele...    32   6.9
Z75531_3(Z75531|pid:none) Caenorhabditis elegans Cosmid C54D10, ...    32   6.9

>AC116987_6(AC116987|pid:none) Dictyostelium discoideum chromosome 2
           map 3527441-3568052 strain AX4, complete sequence.
          Length = 293

 Score =  124 bits (310), Expect = 1e-27
 Identities = 68/108 (62%), Positives = 68/108 (62%)
 Frame = +1

Query: 19  RFXXXAFXXXXAYXRWVGPXYNXKIIPXXLSXIXNPIFXSFXXKAXNPXXIXKYKTPXGN 198
           RF   AF    AY RWV P YN KIIP  LS I NPIF SF  KA N   I KYKT  GN
Sbjct: 147 RFIDQAFTYLSAYIRWVVPEYNEKIIPRLLSSIQNPIFRSFAHKAINQVSIQKYKTQVGN 206

Query: 199 FXLDEXXSXFXSDXNXXSNXLGSKTFIFGGPLSMADIXLFSXLAPIXY 342
           F LDE  S F SD N  SN LGSKTFIFG  LSMADI LFS LA I Y
Sbjct: 207 FSLDEVVSVFKSDLNSLSNLLGSKTFIFGDHLSMADISLFSTLAQIYY 254

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: 3204285
Number of Hits to DB: 252,879,692
Number of extensions: 7509592
Number of successful extensions: 1076
Number of sequences better than 10.0: 4
Number of HSP's gapped: 1076
Number of HSP's successfully gapped: 4
Length of query: 114
Length of database: 1,040,966,779
Length adjustment: 81
Effective length of query: 33
Effective length of database: 781,419,694
Effective search space: 25786849902
Effective search space used: 25786849902
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: 0.85  gvh: 0.53  alm: 0.41  top: 0.53  tms: 0.00  mit: 0.36  mip: 0.04
 nuc: 0.00  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 

	 32.0 %: mitochondrial
	 32.0 %: nuclear
	 20.0 %: cytoplasmic
	  8.0 %: cytoskeletal
	  4.0 %: extracellular, including cell wall
	  4.0 %: peroxisomal

>> prediction for Contig-U10493-1 is mit
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 1
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