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Dicty_cDB
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
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Contig-U14370-1
Contig ID Contig-U14370-1
Contig update 2002.12.18
Contig sequence 
>Contig-U14370-1 (Contig-U14370-1Q) /CSM_Contig/Contig-U14370-1Q.Seq.d
NNNNNNNNNNATNTCAAATACAATTAAAAAANAAGNTGNTCNAAAAAATG
TNAGAGTAATGATNATTTCCCCNGGTATTGNTGAAACTGAATTACTATCN
CATAATNAATCCNATGAAAAAGTTTTNNACNCATATAATAGTTGGAAANA
TACNTTNAAAGGTCAATCAATGNATCCNTNCAATGNTGCAAATTCAATTN
AATTTATGTATGAAANGCCNCAANAAATT
Gap no gap
Contig length 229
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 U14370
List of clone(s) 

est1=CHJ790Z,1,220
Translated Amino Acid sequence 
XXXXSNTIKKXXXXKNVRVMXISPGIXETELLSHNXSXEKVXXXYNSWKXTXKGQSMXPX
NXANSIXFMYEXPQXI
Translated Amino Acid sequence (All Frames) 
Frame A:
xxxxxkyn*kxxxskkcxsndxfpxyx*n*itix*xix*ksfxxi**lexyxxrsinxsx
qxckfnxiyv*xaxxn


Frame B:
XXXXSNTIKKXXXXKNVRVMXISPGIXETELLSHNXSXEKVXXXYNSWKXTXKGQSMXPX
NXANSIXFMYEXPQXI


Frame C:
xxxxqiqlkxkxxxkmxe**xfpxvlxklnyyxixnpmkkfxthiivgxixxkvnqxixx
mxqiqxnlcmkxxxk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U14370-1 (Contig-U14370-1Q)
/CSM_Contig/Contig-U14370-1Q.Seq.d
         (229 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U14370-1 (Contig-U14370-1Q) /CSM_Contig/Conti...   280  6e-76
Contig-U02162-1 (Contig-U02162-1Q) /CSM_Contig/Conti...    36  0.015
Contig-U14670-1 (Contig-U14670-1Q) /CSM_Contig/Conti...    32  0.24
Contig-U12590-1 (Contig-U12590-1Q) /CSM_Contig/Conti...    32  0.24
Contig-U02182-1 (Contig-U02182-1Q) /CSM_Contig/Conti...    32  0.24
Contig-U14742-1 (Contig-U14742-1Q) /CSM_Contig/Conti...    30  0.95
Contig-U13829-1 (Contig-U13829-1Q) /CSM_Contig/Conti...    30  0.95
Contig-U13813-1 (Contig-U13813-1Q) /CSM_Contig/Conti...    30  0.95
Contig-U13781-1 (Contig-U13781-1Q) /CSM_Contig/Conti...    30  0.95
Contig-U12276-1 (Contig-U12276-1Q) /CSM_Contig/Conti...    30  0.95

>Contig-U14370-1 (Contig-U14370-1Q) /CSM_Contig/Contig-U14370-1Q.Seq.d
          Length = 229

 Score =  280 bits (141), Expect = 6e-76
 Identities = 216/216 (100%)
 Strand = Plus / Plus

                                                                       
Query: 14  tcaaatacaattaaaaaanaagntgntcnaaaaaatgtnagagtaatgatnatttccccn 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 14  tcaaatacaattaaaaaanaagntgntcnaaaaaatgtnagagtaatgatnatttccccn 73

                                                                       
Query: 74  ggtattgntgaaactgaattactatcncataatnaatccnatgaaaaagttttnnacnca 133
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 74  ggtattgntgaaactgaattactatcncataatnaatccnatgaaaaagttttnnacnca 133

                                                                       
Query: 134 tataatagttggaaanatacnttnaaaggtcaatcaatgnatccntncaatgntgcaaat 193
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 134 tataatagttggaaanatacnttnaaaggtcaatcaatgnatccntncaatgntgcaaat 193

                                               
Query: 194 tcaattnaatttatgtatgaaangccncaanaaatt 229
           ||||||||||||||||||||||||||||||||||||
Sbjct: 194 tcaattnaatttatgtatgaaangccncaanaaatt 229


>Contig-U02162-1 (Contig-U02162-1Q) /CSM_Contig/Contig-U02162-1Q.Seq.d
          Length = 610

 Score = 36.2 bits (18), Expect = 0.015
 Identities = 18/18 (100%)
 Strand = Plus / Plus

                            
Query: 14 tcaaatacaattaaaaaa 31
          ||||||||||||||||||
Sbjct: 37 tcaaatacaattaaaaaa 54


>Contig-U14670-1 (Contig-U14670-1Q) /CSM_Contig/Contig-U14670-1Q.Seq.d
          Length = 825

 Score = 32.2 bits (16), Expect = 0.24
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                           
Query: 14  tcaaatacaattaaaa 29
           ||||||||||||||||
Sbjct: 697 tcaaatacaattaaaa 712


  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: 1140
Number of Sequences: 6905
Number of extensions: 1140
Number of successful extensions: 357
Number of sequences better than 10.0: 34
length of query: 229
length of database: 5,674,871
effective HSP length: 15
effective length of query: 214
effective length of database: 5,571,296
effective search space: 1192257344
effective search space used: 1192257344
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 2008.12.21
Homology vs DNA 
Query= Contig-U14370-1 (Contig-U14370-1Q) /CSM_Contig/Contig-U14370-1Q.Seq.d
         (229 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

(BJ381520) Dictyostelium discoideum cDNA clone:ddc41d23, 3' ...   280   2e-71  1

>(BJ381520) Dictyostelium discoideum cDNA clone:ddc41d23, 3' end,
           single read.
          Length = 220

 Score =  280 bits (141), Expect = 2e-71
 Identities = 216/216 (100%)
 Strand = Plus / Minus


Query: 14  tcaaatacaattaaaaaanaagntgntcnaaaaaatgtnagagtaatgatnatttccccn 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 217 tcaaatacaattaaaaaanaagntgntcnaaaaaatgtnagagtaatgatnatttccccn 158


Query: 74  ggtattgntgaaactgaattactatcncataatnaatccnatgaaaaagttttnnacnca 133
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 157 ggtattgntgaaactgaattactatcncataatnaatccnatgaaaaagttttnnacnca 98


Query: 134 tataatagttggaaanatacnttnaaaggtcaatcaatgnatccntncaatgntgcaaat 193
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 97  tataatagttggaaanatacnttnaaaggtcaatcaatgnatccntncaatgntgcaaat 38


Query: 194 tcaattnaatttatgtatgaaangccncaanaaatt 229
           ||||||||||||||||||||||||||||||||||||
Sbjct: 37  tcaattnaatttatgtatgaaangccncaanaaatt 2

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 108,909,719
Number of extensions: 6254200
Number of successful extensions: 978873
Number of sequences better than 10.0: 1
Length of query: 229
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 206
Effective length of database: 93,106,754,628
Effective search space: 19179991453368
Effective search space used: 19179991453368
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7.11
Homology vs Protein 
Query= Contig-U14370-1 (Contig-U14370-1Q) /CSM_Contig/Contig-U14370-1Q.Seq.d
         (229 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AE005176_1480(AE005176|pid:none) Lactococcus lactis subsp. lacti...    59   5e-08
CP000422_522(CP000422|pid:none) Pediococcus pentosaceus ATCC 257...    58   9e-08
AJ749949_1201(AJ749949|pid:none) Francisella tularensis subsp. t...    55   6e-07
CP000425_1437(CP000425|pid:none) Lactococcus lactis subsp. cremo...    54   2e-06
AM406671_1004(AM406671|pid:none) Lactococcus lactis subsp. cremo...    54   2e-06
CP000915_633(CP000915|pid:none) Francisella tularensis subsp. me...    54   2e-06
AM233362_742(AM233362|pid:none) Francisella tularensis subsp. ho...    54   2e-06
CP000439_1153(CP000439|pid:none) Francisella tularensis subsp. n...    54   2e-06
CP000817_3998(CP000817|pid:none) Lysinibacillus sphaericus C3-41...    53   4e-06
CP000083_4794(CP000083|pid:none) Colwellia psychrerythraea 34H, ...    53   4e-06
CR378663_127(CR378663|pid:none) Photobacterium profundum SS9; se...    49   7e-05
BA000038_253(BA000038|pid:none) Vibrio vulnificus YJ016 DNA, chr...    49   7e-05
CP000937_93(CP000937|pid:none) Francisella philomiragia subsp. p...    49   7e-05
AE016796_1318(AE016796|pid:none) Vibrio vulnificus CMCP6 chromos...    49   7e-05
CP000094_4320(CP000094|pid:none) Pseudomonas fluorescens Pf0-1, ...    48   9e-05
BA000032_1275(BA000032|pid:none) Vibrio parahaemolyticus RIMD 22...    48   1e-04
CP000758_905(CP000758|pid:none) Ochrobactrum anthropi ATCC 49188...    48   1e-04
CP000926_3240(CP000926|pid:none) Pseudomonas putida GB-1, comple...    45   8e-04
CP000891_476(CP000891|pid:none) Shewanella baltica OS195, comple...    44   0.002
CT573326_1195(CT573326|pid:none) Pseudomonas entomophila str. L4...    44   0.002
AE014299_4027(AE014299|pid:none) Shewanella oneidensis MR-1, com...    44   0.002
CP001154_2856(CP001154|pid:none) Laribacter hongkongensis HLHK9,...    42   0.005
CP000472_4367(CP000472|pid:none) Shewanella piezotolerans WP3, c...    42   0.007
AE016825_2565(AE016825|pid:none) Chromobacterium violaceum ATCC ...    41   0.015
BX293980_289(BX293980|pid:none) Mycoplasma mycoides subsp. mycoi...    33   3.1
CP000806_3910(CP000806|pid:none) Cyanothece sp. ATCC 51142 circu...    33   4.1
CU179680_413(CU179680|pid:none) Mycoplasma agalactiae PG2 chromo...    32   9.1
CP000480_5381(CP000480|pid:none) Mycobacterium smegmatis str. MC...    32   9.1

>AE005176_1480(AE005176|pid:none) Lactococcus lactis subsp. lactis
           Il1403, complete genome.  &AE006378_7(AE006378|pid:none)
           &H86809(H86809)
          Length = 259

 Score = 58.9 bits (141), Expect = 5e-08
 Identities = 27/72 (37%), Positives = 42/72 (58%)
 Frame = +2

Query: 14  SNTIKKXXXXKNVRVMXISPGIXETELLSHNXSXEKVXXXYNSWKXTXKGQSMXPXNXAN 193
           S TI++    KNVR+  ++PG  ETELL+H  + E     YN WK +  G ++ P   A
Sbjct: 175 SETIREEVSGKNVRISLVAPGAAETELLTH-VTDESALNDYNLWKESMGGTTLAPERVAQ 233

Query: 194 SIXFMYEXPQXI 229
           ++ F+Y+ PQ +
Sbjct: 234 TVKFIYDMPQTV 245

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: 160,002,911
Number of extensions: 3796140
Number of successful extensions: 1591
Number of sequences better than 10.0: 28
Number of HSP's gapped: 1587
Number of HSP's successfully gapped: 28
Length of query: 76
Length of database: 1,051,180,864
Length adjustment: 47
Effective length of query: 29
Effective length of database: 899,062,591
Effective search space: 26072815139
Effective search space used: 26072815139
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: 27 (15.0 bits)
PSORT 

 psg: 0.70  gvh: 0.42  alm: 0.51  top: 0.53  tms: 0.00  mit: 0.37  mip: 0.04
 nuc: 0.00  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 

	 56.0 %: mitochondrial
	 20.0 %: nuclear
	 16.0 %: cytoplasmic
	  4.0 %: cytoskeletal
	  4.0 %: peroxisomal

>> prediction for Contig-U14370-1 is mit
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) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 1
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0