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Dicty_cDB
Contig List | Clone List | cDNA Library List
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Atlas | Atlas Image List
NBDC - LSDB Archive
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Dicty_cDB
Contig List | Clone List | cDNA Library List
Atlas
Atlas | Atlas Image List
Contig-U04672-1
Contig ID Contig-U04672-1
Contig update 2001. 8.29
Contig sequence 
>Contig-U04672-1 (Contig-U04672-1Q) /CSM_Contig/Contig-U04672-1Q.Seq.d
ATAAAATTAAAGAGATAATTAAAAAAAATAAAAAATAAAAAAATAAAATA
AAATATAAAATAAAATAAAATAATATAAAAAGATAATTGTATAATAGATA
GATTATGCTATAGAAATGGCAATAACAAATGCATATTATGATTATTCACA
TATAGCATTAATTTCTTTATATACAATATTAGCTATTTTATCAATAATAA
GTTTTATAAGATCAACGACCAAAAAAAATATTTTTATAATATCTTTTCAT
ATAGTTTTACTTATAGCGTCATTATTAAGGGCGGTATCATTTTCACTTTT
NNNAANAAANGANGAAAANGTTAAAGAAACTNGATGGTAATCNATTGNTT
CNAACNAATGAATTNCCTAGTCNNTTTTNATTTAACCTNTTTNTCAATGG
CTTTACTTTTATCAATTCAAATTTTTCAAGGAACATTAGTAGNTAAAGCA
GTAGATATGCCAAAAATNAAAAACAGTTGTCATTATTGCAAATGTTGTTA
TTTATTTAATACTGGCAATTTTATNCATTTTGGATTTTGTATTATTTCCA
TATGAAACAGCATCAGTTGATCAACCAACTTCAGTTTTTCAAATGATCAT
ACAATTCATTGCAGCTNTTATTTATTTTATTACTGCTGTTACTTTCTTTG
TATTTTTATTTAAAACTTATTATGAACATTATGATGATAAATTTGCAGAT
GCAGTTAAAACACAAGAATCTGTACAACTTAAAAAGAGAAGTAATGGAAT
TATATNTTTNTCATTTTTATGTTTTTTAATTAGGGCCATAATGACATGTT
TGACAATATTTTTGAAATTGGGTTTTTGGTATAAGGATTTAGTATATTAT
CTTTTCTTTGAAATCATTCCAATCAGTCTTTTACTTTTTATCATCAATGA
AATGACATATAAAGCTGGAAATATTGTTTTTGGTGGTCATCAATATTCTG
AAGTAACCGAAAATTCAAGATTAACTGAAACTTCCAATTATTTAATTGCT
AAATATTCAAATTCTCAAATTTCAAATATTAATAAATAATAATTTATTAT
GAATAAAATGGGATTTTGTGTTGAAAATATTAATAAATATACTAAAAAAA
AAAAAAAAGTAAAAAAAAAAAAAAAAAAACAAATTGTTTTTTTAAACAAA
AAAGGAAAAAAATAAAAATAAAATAAAAATAAAATAAAAAAAAATAAAAA
AAAAAAAACAATACTTAGAAAGAGTAAAATC
Gap no gap
Contig length 1231
Chromosome number (1..6, M) 5
Chromosome length 5062330
Start point 54616
End point 53385
Strand (PLUS/MINUS) MINUS
Number of clones 2
Number of EST 2
Link to clone list U04672
List of clone(s) 

est1=SSC432E,1,1093
est2=SSC265Z,777,1232
Translated Amino Acid sequence 
*n*rdn*kk*kikk*nki*nkik*ykkiiv**idyaiemaitnayydyshialislytil
ailsiisfirsttkknifiisfhivlliasllravsfslxxxxxexvketxw*sixsnx*
ix*sxxi*pxxqwlyfyqfkffkeh**xkq*ICQKXKTVVIIANVVIYLILAILXILDFV
LFPYETASVDQPTSVFQMIIQFIAAXIYFITAVTFFVFLFKTYYEHYDDKFADAVKTQES
VQLKKRSNGIIXXSFLCFLIRAIMTCLTIFLKLGFWYKDLVYYLFFEIIPISLLLFIINE
MTYKAGNIVFGGHQYSEVTENSRLTETSNYLIAKYSNSQISNINK**fimnkmgfcveni
nkytkkkkkvkkkkkkqivflnkkgkk*k*nknkikknkkkktilrkski
Translated Amino Acid sequence (All Frames) 
Frame A:
iklkr*lkkiknkkik*nik*nkii*kdnciidrlcyrngnnkcil*lftysinffiyni
syfinnkfykindqkkyfynifsysftysviikggiiftfxxkxxkx*rnxmvixxfxxm
nxlvxfxltxxsmalllsiqifqgtlvxkavdmpkxknschyckccylfntgnfxhfgfc
iisi*nsis*stnfsfsndhtihcsxylfyyccyflcifi*nll*tl***icrcs*ntri
ctt*kek*wnyxfxifmffn*ghndmfdnifeigflv*gfsilsfl*nhsnqsftfyhq*
ndi*swkycfwwssif*snrkfkin*nfqlfnc*ifkfsnfky**iiiyye*ngilc*ky
**iy*kkkkskkkkkktncffkqkrkkikik*k*nkkk*kkknnt*ke*n


Frame B:
*n*rdn*kk*kikk*nki*nkik*ykkiiv**idyaiemaitnayydyshialislytil
ailsiisfirsttkknifiisfhivlliasllravsfslxxxxxexvketxw*sixsnx*
ix*sxxi*pxxqwlyfyqfkffkeh**xkq*ICQKXKTVVIIANVVIYLILAILXILDFV
LFPYETASVDQPTSVFQMIIQFIAAXIYFITAVTFFVFLFKTYYEHYDDKFADAVKTQES
VQLKKRSNGIIXXSFLCFLIRAIMTCLTIFLKLGFWYKDLVYYLFFEIIPISLLLFIINE
MTYKAGNIVFGGHQYSEVTENSRLTETSNYLIAKYSNSQISNINK**fimnkmgfcveni
nkytkkkkkvkkkkkkqivflnkkgkk*k*nknkikknkkkktilrkski


Frame C:
kikeiikknkk*knkikykik*nnikr*lynr*iml*kwq*qmhimiihi*h*flyiqy*
lfyq**vl*dqrpkkifl*ylfi*fyl*rhy*gryhfhfxxxxxkxlkkldgnxlxxtne
xpsxfxfnlfxngftfinsnfsrnisx*ssryaknxkqlsllqmllfi*ywqfyxfwily
yfhmkqhqlinqlqffk*synslqllfillllllslyfylklimnimminlqmqlkhknl
ynlkrevmelyxxhfyvf*lgp**hv*qyf*nwvfgiri*yiifslksfqsvfyflssmk
*hikleilflvvinilk*pkiqd*lklpii*llniqilkfqilinnnll*ikwdfvlkil
inilkkkkk*kkkkknklff*tkkeknknkikik*kkikkkkqylervk
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U04672-1 (Contig-U04672-1Q)
/CSM_Contig/Contig-U04672-1Q.Seq.d
         (1231 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U04672-1 (Contig-U04672-1Q) /CSM_Contig/Conti...   817  0.0
Contig-U10523-1 (Contig-U10523-1Q) /CSM_Contig/Conti...    34  0.34
Contig-U10328-1 (Contig-U10328-1Q) /CSM_Contig/Conti...    34  0.34
Contig-U06662-1 (Contig-U06662-1Q) /CSM_Contig/Conti...    34  0.34
Contig-U01253-1 (Contig-U01253-1Q) /CSM_Contig/Conti...    34  0.34
Contig-U14510-1 (Contig-U14510-1Q) /CSM_Contig/Conti...    32  1.4
Contig-U14343-1 (Contig-U14343-1Q) /CSM_Contig/Conti...    32  1.4
Contig-U13941-1 (Contig-U13941-1Q) /CSM_Contig/Conti...    32  1.4
Contig-U13910-1 (Contig-U13910-1Q) /CSM_Contig/Conti...    32  1.4
Contig-U12712-1 (Contig-U12712-1Q) /CSM_Contig/Conti...    32  1.4

>Contig-U04672-1 (Contig-U04672-1Q) /CSM_Contig/Contig-U04672-1Q.Seq.d
          Length = 1231

 Score =  817 bits (412), Expect = 0.0
 Identities = 513/532 (96%)
 Strand = Plus / Plus

                                                                       
Query: 82  gataattgtataatagatagattatgctatagaaatggcaataacaaatgcatattatga 141
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 82  gataattgtataatagatagattatgctatagaaatggcaataacaaatgcatattatga 141

                                                                       
Query: 142 ttattcacatatagcattaatttctttatatacaatattagctattttatcaataataag 201
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 142 ttattcacatatagcattaatttctttatatacaatattagctattttatcaataataag 201

                                                                       
Query: 202 ttttataagatcaacgaccnnnnnnnntatttttataatatcttttcatatagttttact 261
           |||||||||||||||||||        |||||||||||||||||||||||||||||||||
Sbjct: 202 ttttataagatcaacgaccaaaaaaaatatttttataatatcttttcatatagttttact 261

                                                                       
Query: 262 tatagcgtcattattaagggcggtatcattttcacttttnnnaanaaangangaaaangt 321
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 262 tatagcgtcattattaagggcggtatcattttcacttttnnnaanaaangangaaaangt 321

                                                                       
Query: 322 taaagaaactngatggtaatcnattgnttcnaacnaatgaattncctagtcnnttttnat 381
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 322 taaagaaactngatggtaatcnattgnttcnaacnaatgaattncctagtcnnttttnat 381

                                                                       
Query: 382 ttaacctntttntcaatggctttacttttatcaattcaaatttttcaaggaacattagta 441
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 382 ttaacctntttntcaatggctttacttttatcaattcaaatttttcaaggaacattagta 441

                                                                       
Query: 442 gntaaagcagtagatatgccnnnnnnnnnnnncagttgtcattattgcaaatgttgttat 501
           ||||||||||||||||||||      |     ||||||||||||||||||||||||||||
Sbjct: 442 gntaaagcagtagatatgccaaaaatnaaaaacagttgtcattattgcaaatgttgttat 501

                                                                       
Query: 502 ttatttaatactggcaattttatncattttggattttgtattatttccatatgaaacagc 561
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 502 ttatttaatactggcaattttatncattttggattttgtattatttccatatgaaacagc 561

                                                               
Query: 562 atcagttgatcaaccaacttcagtttttcaaatgatcatacaattcattgca 613
           ||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 562 atcagttgatcaaccaacttcagtttttcaaatgatcatacaattcattgca 613


 Score =  426 bits (215), Expect = e-119
 Identities = 215/215 (100%)
 Strand = Plus / Plus

                                                                       
Query: 778 aattagggccataatgacatgtttgacaatatttttgaaattgggtttttggtataagga 837
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 778 aattagggccataatgacatgtttgacaatatttttgaaattgggtttttggtataagga 837

                                                                       
Query: 838 tttagtatattatcttttctttgaaatcattccaatcagtcttttactttttatcatcaa 897
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 838 tttagtatattatcttttctttgaaatcattccaatcagtcttttactttttatcatcaa 897

                                                                       
Query: 898 tgaaatgacatataaagctggaaatattgtttttggtggtcatcaatattctgaagtaac 957
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 898 tgaaatgacatataaagctggaaatattgtttttggtggtcatcaatattctgaagtaac 957

                                              
Query: 958 cgaaaattcaagattaactgaaacttccaattatt 992
           |||||||||||||||||||||||||||||||||||
Sbjct: 958 cgaaaattcaagattaactgaaacttccaattatt 992


 Score =  165 bits (83), Expect = 1e-40
 Identities = 83/83 (100%)
 Strand = Plus / Plus

                                                                       
Query: 673 tgaacattatgatgataaatttgcagatgcagttaaaacacaagaatctgtacaacttaa 732
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 673 tgaacattatgatgataaatttgcagatgcagttaaaacacaagaatctgtacaacttaa 732

                                  
Query: 733 aaagagaagtaatggaattatat 755
           |||||||||||||||||||||||
Sbjct: 733 aaagagaagtaatggaattatat 755


 Score = 46.1 bits (23), Expect = 9e-05
 Identities = 23/23 (100%)
 Strand = Plus / Plus

                                   
Query: 1209 caatacttagaaagagtaaaatc 1231
            |||||||||||||||||||||||
Sbjct: 1209 caatacttagaaagagtaaaatc 1231


 Score = 38.2 bits (19), Expect = 0.022
 Identities = 19/19 (100%)
 Strand = Plus / Plus

                             
Query: 1  ataaaattaaagagataat 19
          |||||||||||||||||||
Sbjct: 1  ataaaattaaagagataat 19


>Contig-U10523-1 (Contig-U10523-1Q) /CSM_Contig/Contig-U10523-1Q.Seq.d
          Length = 548

 Score = 34.2 bits (17), Expect = 0.34
 Identities = 23/25 (92%)
 Strand = Plus / Plus

                                    
Query: 402 tttacttttatcaattcaaattttt 426
           ||||||||||||||||  |||||||
Sbjct: 279 tttacttttatcaattttaattttt 303


>Contig-U10328-1 (Contig-U10328-1Q) /CSM_Contig/Contig-U10328-1Q.Seq.d
          Length = 1351

 Score = 34.2 bits (17), Expect = 0.34
 Identities = 17/17 (100%)
 Strand = Plus / Plus

                             
Query: 724  acaacttaaaaagagaa 740
            |||||||||||||||||
Sbjct: 1203 acaacttaaaaagagaa 1219


  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: 13,737
Number of Sequences: 6905
Number of extensions: 13737
Number of successful extensions: 1324
Number of sequences better than 10.0: 94
length of query: 1231
length of database: 5,674,871
effective HSP length: 16
effective length of query: 1215
effective length of database: 5,564,391
effective search space: 6760735065
effective search space used: 6760735065
T: 0
A: 40
X1: 6 (11.9 bits)
X2: 15 (29.7 bits)
S1: 12 (24.3 bits)
S2: 15 (30.2 bits)
dna update 2009. 6.28
Homology vs DNA 
Query= Contig-U04672-1 (Contig-U04672-1Q) /CSM_Contig/Contig-U04672-1Q.Seq.d
         (1231 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

(AU051937) Dictyostelium discoideum slug cDNA, clone SSC432.      311   0.0    5
(BJ329417) Dictyostelium discoideum cDNA clone:dda24k24, 5' ...   188   e-164  5
(C84022) Dictyostelium discoideum slug cDNA, clone SSC265.        283   1e-77  2
(AU071745) Dictyostelium discoideum slug cDNA, clone SSC432.      188   4e-47  2
(AC120090) Rattus norvegicus clone CH230-498I1, *** SEQUENCI...    52   0.052  1
(AC107109) Rattus norvegicus clone CH230-16K10, *** SEQUENCI...    52   0.052  1
(DH739361) Rattus norvegicus DNA, BAC clone: RNB1-313B10, 5'...    52   0.052  1
(AC124706) Mus musculus BAC clone RP24-69G17 from chromosome...    50   0.21   1
(BH109156) RPCI-24-401O23.TJ RPCI-24 Mus musculus genomic cl...    50   0.21   1
(GD051936) CCHZ30843.b1 CCHZ Panicum virgatum abiotic and bi...    50   0.21   1
(FL918470) CCGO11766.g1 CCGO Panicum virgatum root (H) Panic...    50   0.21   1
(FL748875) CCGC3364.b1 CCGC Panicum virgatum early floral bu...    50   0.21   1
(FL716208) CCGB3179.b1 CCGB Panicum virgatum apex + stem (L)...    50   0.21   1
(FL695027) CCGA4099.b1 CCGA Panicum virgatum apex + stem (H)...    50   0.21   1
(CO131906) GR__Eb44H02.f GR__Eb Gossypium raimondii cDNA clo...    40   0.74   2
(CO110349) GR__Eb0044H02.f GR__Eb Gossypium raimondii cDNA c...    40   0.74   2
(AC162967) Bos taurus clone CH240-127N19, WORKING DRAFT SEQU...    48   0.81   1
(CO108558) GR__Eb0040H04.f GR__Eb Gossypium raimondii cDNA c...    40   0.85   2
(DD010735) Diagnosis of known genetic Parameters within the ...    32   1.4    2
(AX344550) Sequence 1 from Patent WO0200932.                       32   1.6    2
(FB763448) Sequence 313 from Patent WO2008031133.                  38   1.6    2
(DH733531) Rattus norvegicus DNA, BAC clone: RNB1-305D14, 3'...    36   3.0    2
(FM992690) Candida dubliniensis CD36 chromosome 3, complete ...    46   3.2    1
(AC018928) Genomic Sequence For Arabidopsis thaliana Clone F...    46   3.2    1
(AC006918) Arabidopsis thaliana chromosome 2 clone F18P14 ma...    46   3.2    1
(DD000815) PLANT ARTIFICIAL CHROMOSOME COMPOSITIONS AND METH...    46   3.2    1
(AX059500) Sequence 233 from Patent WO0055325.                     46   3.2    1
(AR777049) Sequence 204 from patent US 6972197.                    46   3.2    1
(AR549066) Sequence 4197 from patent US 6747137.                   46   3.2    1
(AC155960) Xenopus (Silurana) tropicalis clone CH216-1D15, W...    46   3.2    1
(BH241633) AUILD63TR AUIL Arabidopsis thaliana genomic clone...    46   3.2    1
(BH241135) AUILG57TR AUIL Arabidopsis thaliana genomic clone...    46   3.2    1
(FI277265) GT23959.Ds5.05.20.2008.jz37.647 Arabidopsis thali...    46   3.2    1
(CW978764) KBrH001C17R KBrH, Brassica rapa HindIII BAC libra...    46   3.2    1
(AC018787) Homo sapiens, clone RP11-22O12, complete sequence.      38   3.7    3
(EJ719560) 1092959442704 Global-Ocean-Sampling_GS-30-02-01-1...    42   4.1    2
(AC015558) Homo sapiens chromosome 15 clone RP11-301A18, WOR...    38   5.1    6
(AL096863) Human DNA sequence from clone RP5-1119I23 on chro...    32   6.2    2
(CT990558) S.lycopersicum DNA sequence from clone LE_HBa-308...    40   7.9    3
(FH080075) CHO_OF3708xg11r1.ab1 CHO_OF3 Nicotiana tabacum ge...    34   8.0    2
(FH378843) CHO_OF4728xm15f1.ab1 CHO_OF4 Nicotiana tabacum ge...    34   8.1    2
(CD299126) AGENCOURT_14250572 NIH_MGC_187 Homo sapiens cDNA ...    32   8.1    2
(FH743705) CHO_OF5169xf12f1.ab1 CHO_OF5 Nicotiana tabacum ge...    34   8.1    2
(CT043677) Sus scrofa genomic clone PigE-209L17, genomic sur...    32   8.4    2

>(AU051937) Dictyostelium discoideum slug cDNA, clone SSC432.
          Length = 791

 Score =  311 bits (157), Expect(5) = 0.0
 Identities = 157/157 (100%)
 Strand = Plus / Plus


Query: 828 ggtataaggatttagtatattatcttttctttgaaatcattccaatcagtcttttacttt 887
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 526 ggtataaggatttagtatattatcttttctttgaaatcattccaatcagtcttttacttt 585


Query: 888 ttatcatcaatgaaatgacatataaagctggaaatattgtttttggtggtcatcaatatt 947
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 586 ttatcatcaatgaaatgacatataaagctggaaatattgtttttggtggtcatcaatatt 645


Query: 948 ctgaagtaaccgaaaattcaagattaactgaaacttc 984
           |||||||||||||||||||||||||||||||||||||
Sbjct: 646 ctgaagtaaccgaaaattcaagattaactgaaacttc 682

 Score =  220 bits (111), Expect(5) = 0.0
 Identities = 157/180 (87%)
 Strand = Plus / Plus


Query: 307 aaangangaaaangttaaagaaactngatggtaatcnattgnttcnaacnaatgaattnc 366
           ||| || ||||| | ||||| |||| |||||||| | |||| ||| ||| |||||||| |
Sbjct: 7   aaacgaggaaaaggntaaagnaactcgatggtaanccattggttccaaccaatgaattcc 66


Query: 367 ctagtcnnttttnatttaacctntttntcaatggctttacttttatcaattcaaattttt 426
           |||| |  |  | ||||||||| ||| |||||||||||||||||||||||||||||||||
Sbjct: 67  ctagnccctnntcatttaacctctttctcaatggctttacttttatcaattcaaattttt 126


Query: 427 caaggaacattagtagntaaagcagtagatatgccaaaaatnaaaaacagttgtcattat 486
           |||||||||||||||| |||||||||||||| ||||||||| ||||||||||||||||||
Sbjct: 127 caaggaacattagtaggtaaagcagtagatangccaaaaatcaaaaacagttgtcattat 186

 Score =  174 bits (88), Expect(5) = 0.0
 Identities = 90/91 (98%)
 Strand = Plus / Plus


Query: 526 cattttggattttgtattatttccatatgaaacagcatcagttgatcaaccaacttcagt 585
           ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 224 cattttggattttgtattattnccatatgaaacagcatcagttgatcaaccaacttcagt 283


Query: 586 ttttcaaatgatcatacaattcattgcagct 616
           |||||||||||||||||||||||||||||||
Sbjct: 284 ttttcaaatgatcatacaattcattgcagct 314

 Score =  149 bits (75), Expect(5) = 0.0
 Identities = 81/81 (100%)
 Strand = Plus / Plus


Query: 683 gatgataaatttgcagatgcagttaaaacacaagaatctgtacaacttaaaaagagaagt 742
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 381 gatgataaatttgcagatgcagttaaaacacaagaatctgtacaacttaaaaagagaagt 440


Query: 743 aatggaattatatntttntca 763
           |||||||||||||||||||||
Sbjct: 441 aatggaattatatntttntca 461

 Score = 61.9 bits (31), Expect(5) = 0.0
 Identities = 35/37 (94%)
 Strand = Plus / Plus


Query: 487 tgcaaatgttgttatttatttaatactggcaatttta 523
           ||||||||| || ||||||||||||||||||||||||
Sbjct: 186 tgcaaatgtngtnatttatttaatactggcaatttta 222

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 935,393,578
Number of extensions: 62947290
Number of successful extensions: 4850554
Number of sequences better than 10.0: 44
Length of query: 1231
Length of database: 101,790,757,118
Length adjustment: 24
Effective length of query: 1207
Effective length of database: 99,340,224,878
Effective search space: 119903651427746
Effective search space used: 119903651427746
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7.30
Homology vs Protein 
Query= Contig-U04672-1 (Contig-U04672-1Q) /CSM_Contig/Contig-U04672-1Q.Seq.d
         (1231 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

BT052100_1(BT052100|pid:none) Medicago truncatula clone MTYF9_FA...    46   0.003
AB193041_1(AB193041|pid:none) Solanum lycopersicum LeTH1 mRNA fo...    45   0.005
BT038476_1(BT038476|pid:none) Zea mays full-length cDNA clone ZM...    44   0.009
EU963263_1(EU963263|pid:none) Zea mays clone 260042 unknown mRNA.      44   0.012
BT041243_1(BT041243|pid:none) Zea mays full-length cDNA clone ZM...    44   0.012
H84433(H84433)hypothetical protein At2g02180 [imported] - Arabid...    44   0.016
AB036427_1(AB036427|pid:none) Arabidopsis thaliana mRNA for TOM3...    44   0.016
AB057678_1(AB057678|pid:none) Arabidopsis thaliana mRNA for THH1...    42   0.035
AC010657_3(AC010657|pid:none) Genomic sequence for Arabidopsis t...    42   0.035
EU975512_1(EU975512|pid:none) Zea mays clone 491224 unknown mRNA.      42   0.035
AC105363_1(AC105363|pid:none) Oryza sativa (japonica cultivar-gr...    42   0.059
EU408477_1(EU408477|pid:none) Arachis hypogaea tobamovirus multi...    41   0.078
EF678108_1(EF678108|pid:none) Picea sitchensis clone WS02822_K20...    37   1.9
BT055103_1(BT055103|pid:none) Zea mays full-length cDNA clone ZM...    36   2.5
EU962729_1(EU962729|pid:none) Zea mays clone 245049 tobamovirus ...    36   2.5
BT035975_1(BT035975|pid:none) Zea mays full-length cDNA clone ZM...    36   2.5
BT066277_1(BT066277|pid:none) Zea mays full-length cDNA clone ZM...    36   3.3
BT066755_1(BT066755|pid:none) Zea mays full-length cDNA clone ZM...    36   3.3
EU963184_1(EU963184|pid:none) Zea mays clone 258804 tobamovirus ...    35   4.3
AC084404_3(AC084404|pid:none) Oryza sativa chromosome 3 BAC OSJN...    35   5.6
CR931687_15(CR931687|pid:none) Streptococcus pneumoniae strain 2...    34   9.5

>BT052100_1(BT052100|pid:none) Medicago truncatula clone
           MTYF9_FA_FB_FC1G-B-3 unknown mRNA.
          Length = 294

 Score = 45.8 bits (107), Expect = 0.003
 Identities = 25/58 (43%), Positives = 33/58 (56%), Gaps = 6/58 (10%)
 Frame = +2

Query: 764 FLCFLIRAIMTCLTIFLK------LGFWYKDLVYYLFFEIIPISLLLFIINEMTYKAG 919
           F CFLIR +M C   F K      L     +L+YYL  EI+P SL+LFI+ ++  K G
Sbjct: 229 FSCFLIRCVMMCFNAFDKAADLDVLDHPILNLIYYLLVEILPSSLVLFILRKLPPKRG 286

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: 1,071,285,214
Number of extensions: 15049994
Number of successful extensions: 38286
Number of sequences better than 10.0: 21
Number of HSP's gapped: 38256
Number of HSP's successfully gapped: 21
Length of query: 410
Length of database: 1,061,185,681
Length adjustment: 131
Effective length of query: 279
Effective length of database: 633,018,993
Effective search space: 176612299047
Effective search space used: 176612299047
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: 32 (16.9 bits)
PSORT 

 psg: 0.95  gvh: 0.51  alm: 0.15  top: 0.13  tms: 0.27  mit: 0.27  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: 1.00  m3b: 0.00  m_ : 0.00 

	 32.0 %: endoplasmic reticulum
	 24.0 %: mitochondrial
	 20.0 %: plasma membrane
	  8.0 %: extracellular, including cell wall
	  4.0 %: vacuolar
	  4.0 %: Golgi
	  4.0 %: nuclear
	  4.0 %: vesicles of secretory system

>> prediction for Contig-U04672-1 is end
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) 2
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