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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-U13557-1
Contig ID Contig-U13557-1
Contig update 2002.12.18
Contig sequence 
>Contig-U13557-1 (Contig-U13557-1Q) /CSM_Contig/Contig-U13557-1Q.Seq.d
NNNNNNNNNNGNGTTTTTTNTTGTTTANTGCAANTAANTTTTGGNANTGN
GTTGGGNNCGAAATTTTCAAAGGTAGTCANGCCAGTAAAANACGAANTTT
TACCTGTAANTTTCCCTGANTGGGTAANGTTTATTGTAANTCCGTTNGNT
GCCNTTACATTTGGTGTTCAANTAAAANTTCANTGGAAANAANTTTGGGN
TATCATCATCGNTAGTTACATTGGNGTAACCGTTGGTAANTGGGGTANTA
AANATTTTGGTGANGNTGGNGCTTTNTTTGGNTCANCTGCAATTTGNGCT
TTAGGTAACCNTTACTCAANANTAACAAATANTTTTGCGGTNGTTCCNAN
TANGGCGGGNATTATTTTANTGGNTCCNGGTAGNANGGGTGTTAAAGGNA
TCGTTTCAATCAGTGANGGTGANATTTCCNGANGAATTGATTTCNTTGGT
GGNANGTTTANGACTGCNGCAANTTTAACNATGGGTTTANTGGNTGCNA
Gap no gap
Contig length 499
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 U13557
List of clone(s) 

est1=VHB701Z,1,490
Translated Amino Acid sequence 
XXXXVFXCLXQXXFGXXLGXKFSKVVXPVKXEXLPVXFPXWVXFIVXPXXAXTFGVQXKX
XWKXXWXIIIXSYIGVTVGXWGXKXFGXXGAXFGSXAIXALGNXYSXXTNXFAVVPXXAG
IILXXPGXXGVKGIVSISXGXISXXIDFXGGXFXTAAXLTMGLXXA
Translated Amino Acid sequence (All Frames) 
Frame A:
XXXXVFXCLXQXXFGXXLGXKFSKVVXPVKXEXLPVXFPXWVXFIVXPXXAXTFGVQXKX
XWKXXWXIIIXSYIGVTVGXWGXKXFGXXGAXFGSXAIXALGNXYSXXTNXFAVVPXXAG
IILXXPGXXGVKGIVSISXGXISXXIDFXGGXFXTAAXLTMGLXXA


Frame B:
xxxxffxvxcx*xlxxxwxrnfqr*sxq*xtxfyl*xslxg*xll*xrxxplhlvfx*xf
xgxxfgxsssxvtlx*plvxgvxxilvxxxlxlxxlqfxl*vtxtqx*qixlrxfxxxrx
lfxwxxvxxvlkxsfqsvxvxfpxelislvxxlxlxqx*xwvxwxx


Frame C:
xxxxfxlfxaxxfwxxvgxeifkgsxaskxrxftcxfp*xgxvycxsvxcxyiwcsxkxs
xexxlgyhhr*lhwxnrw*xgx*xfw*xwxfxwxxcnlxfr*pllxxnkxfcgxsxxggx
yfxgsx*xgc*rxrfnq*x*xfxxn*fxwwxvxdcxxfnxgfxgc
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U13557-1 (Contig-U13557-1Q)
/CSM_Contig/Contig-U13557-1Q.Seq.d
         (499 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U13557-1 (Contig-U13557-1Q) /CSM_Contig/Conti...   575  e-164
Contig-U04638-1 (Contig-U04638-1Q) /CSM_Contig/Conti...    32  0.54
Contig-U13949-1 (Contig-U13949-1Q) /CSM_Contig/Conti...    28  8.4
Contig-U11749-1 (Contig-U11749-1Q) /CSM_Contig/Conti...    28  8.4
Contig-U11478-1 (Contig-U11478-1Q) /CSM_Contig/Conti...    28  8.4
Contig-U11146-1 (Contig-U11146-1Q) /CSM_Contig/Conti...    28  8.4
Contig-U10804-1 (Contig-U10804-1Q) /CSM_Contig/Conti...    28  8.4
Contig-U10043-1 (Contig-U10043-1Q) /CSM_Contig/Conti...    28  8.4
Contig-U09782-1 (Contig-U09782-1Q) /CSM_Contig/Conti...    28  8.4

>Contig-U13557-1 (Contig-U13557-1Q) /CSM_Contig/Contig-U13557-1Q.Seq.d
          Length = 499

 Score =  575 bits (290), Expect = e-164
 Identities = 485/485 (100%)
 Strand = Plus / Plus

                                                                       
Query: 13  gttttttnttgtttantgcaantaanttttggnantgngttgggnncgaaattttcaaag 72
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 13  gttttttnttgtttantgcaantaanttttggnantgngttgggnncgaaattttcaaag 72

                                                                       
Query: 73  gtagtcangccagtaaaanacgaanttttacctgtaantttccctgantgggtaangttt 132
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 73  gtagtcangccagtaaaanacgaanttttacctgtaantttccctgantgggtaangttt 132

                                                                       
Query: 133 attgtaantccgttngntgccnttacatttggtgttcaantaaaanttcantggaaanaa 192
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 133 attgtaantccgttngntgccnttacatttggtgttcaantaaaanttcantggaaanaa 192

                                                                       
Query: 193 ntttgggntatcatcatcgntagttacattggngtaaccgttggtaantggggtantaaa 252
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 193 ntttgggntatcatcatcgntagttacattggngtaaccgttggtaantggggtantaaa 252

                                                                       
Query: 253 nattttggtgangntggngctttntttggntcanctgcaatttgngctttaggtaaccnt 312
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 253 nattttggtgangntggngctttntttggntcanctgcaatttgngctttaggtaaccnt 312

                                                                       
Query: 313 tactcaanantaacaaatanttttgcggtngttccnantanggcgggnattattttantg 372
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 313 tactcaanantaacaaatanttttgcggtngttccnantanggcgggnattattttantg 372

                                                                       
Query: 373 gntccnggtagnangggtgttaaaggnatcgtttcaatcagtganggtganatttccnga 432
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 373 gntccnggtagnangggtgttaaaggnatcgtttcaatcagtganggtganatttccnga 432

                                                                       
Query: 433 ngaattgatttcnttggtggnangtttangactgcngcaantttaacnatgggtttantg 492
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 433 ngaattgatttcnttggtggnangtttangactgcngcaantttaacnatgggtttantg 492

                
Query: 493 gntgc 497
           |||||
Sbjct: 493 gntgc 497


>Contig-U04638-1 (Contig-U04638-1Q) /CSM_Contig/Contig-U04638-1Q.Seq.d
          Length = 663

 Score = 32.2 bits (16), Expect = 0.54
 Identities = 16/16 (100%)
 Strand = Plus / Plus

                          
Query: 61 aaattttcaaaggtag 76
          ||||||||||||||||
Sbjct: 38 aaattttcaaaggtag 53


>Contig-U13949-1 (Contig-U13949-1Q) /CSM_Contig/Contig-U13949-1Q.Seq.d
          Length = 1211

 Score = 28.2 bits (14), Expect = 8.4
 Identities = 14/14 (100%)
 Strand = Plus / Plus

                         
Query: 158 catttggtgttcaa 171
           ||||||||||||||
Sbjct: 436 catttggtgttcaa 449


  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: 505
Number of Sequences: 6905
Number of extensions: 505
Number of successful extensions: 26
Number of sequences better than 10.0: 9
length of query: 499
length of database: 5,674,871
effective HSP length: 16
effective length of query: 483
effective length of database: 5,564,391
effective search space: 2687600853
effective search space used: 2687600853
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 2008.12.11
Homology vs DNA 
Query= Contig-U13557-1 (Contig-U13557-1Q) /CSM_Contig/Contig-U13557-1Q.Seq.d
         (499 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

(BJ437352) Dictyostelium discoideum cDNA clone:ddv34b01, 3' ...   573   e-159  1
(AU034130) Dictyostelium discoideum slug cDNA, clone SLB778.      517   e-142  1
(BJ407614) Dictyostelium discoideum cDNA clone:dds43i06, 3' ...   513   e-141  1
(BJ445250) Dictyostelium discoideum cDNA clone:ddv58m20, 3' ...   500   e-137  1
(BJ407306) Dictyostelium discoideum cDNA clone:dds38k02, 3' ...   500   e-137  1
(BJ408333) Dictyostelium discoideum cDNA clone:dds45p11, 3' ...   498   e-136  1
(BJ408987) Dictyostelium discoideum cDNA clone:dds47k16, 3' ...   474   e-129  1
(BJ443199) Dictyostelium discoideum cDNA clone:ddv52o03, 3' ...   470   e-128  1
(C25557) Dictyostelium discoideum slug cDNA, clone SLA296.        444   e-120  1
(BJ352408) Dictyostelium discoideum cDNA clone:dda46l16, 3' ...   442   e-120  1
(AU034523) Dictyostelium discoideum slug cDNA, clone SLC382.      408   e-110  1
(BJ379883) Dictyostelium discoideum cDNA clone:ddc36f10, 3' ...   392   e-105  1
(BJ404623) Dictyostelium discoideum cDNA clone:dds29i05, 3' ...   262   1e-65  1
(BJ408785) Dictyostelium discoideum cDNA clone:dds46o23, 3' ...   250   4e-62  1
(BJ351474) Dictyostelium discoideum cDNA clone:dda43h15, 3' ...   236   6e-58  1
(AU052901) Dictyostelium discoideum slug cDNA, clone SLF291.      190   3e-44  1

>(BJ437352) Dictyostelium discoideum cDNA clone:ddv34b01, 3' end,
           single read.
          Length = 490

 Score =  573 bits (289), Expect = e-159
 Identities = 484/484 (100%)
 Strand = Plus / Minus


Query: 14  ttttttnttgtttantgcaantaanttttggnantgngttgggnncgaaattttcaaagg 73
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 487 ttttttnttgtttantgcaantaanttttggnantgngttgggnncgaaattttcaaagg 428


Query: 74  tagtcangccagtaaaanacgaanttttacctgtaantttccctgantgggtaangttta 133
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 427 tagtcangccagtaaaanacgaanttttacctgtaantttccctgantgggtaangttta 368


Query: 134 ttgtaantccgttngntgccnttacatttggtgttcaantaaaanttcantggaaanaan 193
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 367 ttgtaantccgttngntgccnttacatttggtgttcaantaaaanttcantggaaanaan 308


Query: 194 tttgggntatcatcatcgntagttacattggngtaaccgttggtaantggggtantaaan 253
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 307 tttgggntatcatcatcgntagttacattggngtaaccgttggtaantggggtantaaan 248


Query: 254 attttggtgangntggngctttntttggntcanctgcaatttgngctttaggtaaccntt 313
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 247 attttggtgangntggngctttntttggntcanctgcaatttgngctttaggtaaccntt 188


Query: 314 actcaanantaacaaatanttttgcggtngttccnantanggcgggnattattttantgg 373
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 187 actcaanantaacaaatanttttgcggtngttccnantanggcgggnattattttantgg 128


Query: 374 ntccnggtagnangggtgttaaaggnatcgtttcaatcagtganggtganatttccngan 433
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 127 ntccnggtagnangggtgttaaaggnatcgtttcaatcagtganggtganatttccngan 68


Query: 434 gaattgatttcnttggtggnangtttangactgcngcaantttaacnatgggtttantgg 493
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 67  gaattgatttcnttggtggnangtttangactgcngcaantttaacnatgggtttantgg 8


Query: 494 ntgc 497
           ||||
Sbjct: 7   ntgc 4

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 109,483,261
Number of extensions: 4839206
Number of successful extensions: 99661
Number of sequences better than 10.0: 16
Length of query: 499
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 476
Effective length of database: 93,106,754,628
Effective search space: 44318815202928
Effective search space used: 44318815202928
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)
protein update 2009. 7. 7
Homology vs Protein 
Query= Contig-U13557-1 (Contig-U13557-1Q) /CSM_Contig/Contig-U13557-1Q.Seq.d
         (499 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

CP000931_3992(CP000931|pid:none) Shewanella halifaxensis HAW-EB4...    39   0.052
CP000472_2031(CP000472|pid:none) Shewanella piezotolerans WP3, c...    36   0.58
AE014299_306(AE014299|pid:none) Shewanella oneidensis MR-1, comp...    32   6.4
CP000444_272(CP000444|pid:none) Shewanella sp. MR-7, complete ge...    32   6.4
CP000563_4021(CP000563|pid:none) Shewanella baltica OS155, compl...    32   6.4

>CP000931_3992(CP000931|pid:none) Shewanella halifaxensis HAW-EB4,
           complete genome.
          Length = 406

 Score = 39.3 bits (90), Expect = 0.052
 Identities = 29/123 (23%), Positives = 42/123 (34%), Gaps = 1/123 (0%)
 Frame = +1

Query: 16  FXCLXQXXFGXXLGXKFSKVVXPVKXEXLPVXFPXWVXFIVXPXXAXTFGVQXKXXWKXX 195
           F  L +  FG  LG    K +        P   P W  FI  P  +    +  K   K
Sbjct: 234 FMLLFKLYFGVILGMAIGKALFDETTYIPPAVLPQWAVFISVPILSMALVIIFKARMKDS 293

Query: 196 WXIIIXSYIGVTVGXWGXKXFGXX-GAXFGSXAIXALGNXYSXXTNXFAVVPXXAGIILX 372
              I+   +       G   FG   G  FG+ A+    N ++      A +    GI++
Sbjct: 294 PWGILAGTVAFFSAMLGGLYFGESIGIFFGALAVGIYSNLFARWMKAPASIALLQGIVIL 353

Query: 373 XPG 381
            PG
Sbjct: 354 VPG 356

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: 319,419,429
Number of extensions: 3923440
Number of successful extensions: 1112
Number of sequences better than 10.0: 5
Number of HSP's gapped: 1111
Number of HSP's successfully gapped: 5
Length of query: 166
Length of database: 1,051,180,864
Length adjustment: 119
Effective length of query: 47
Effective length of database: 666,030,343
Effective search space: 31303426121
Effective search space used: 31303426121
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: 30 (16.2 bits)
PSORT 

 psg: 0.84  gvh: 0.58  alm: 0.41  top: 0.60  tms: 0.00  mit: 0.23  mip: 0.00
 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 

	 48.0 %: cytoplasmic
	 28.0 %: nuclear
	  8.0 %: cytoskeletal
	  8.0 %: mitochondrial
	  4.0 %: Golgi
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U13557-1 is cyt
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