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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-U12987-1
Contig ID Contig-U12987-1
Contig update 2002.12.18
Contig sequence 
>Contig-U12987-1 (Contig-U12987-1Q) /CSM_Contig/Contig-U12987-1Q.Seq.d
ATATATATAAAATAATTAGTATAATGTCAAGTGGTGATAGTAATTTAAAG
AGAAGAAGAGGAGGAAATACTGGTCAATCATCAAAATCATATAATACATG
GACTGATTATGAAGAAGATTTAGAAGAATCTGGTGAATTTAATCAATCAA
TAAAAAAAACAACAAATACATCAAGTGCAACATTAACATCATCAGAAGAA
AAAGGATCACTTTTAGATTATTCAAAGAGGTGTATATTAAAACAAGATAA
TAAATCAAGACCAATTTGGGTTTGTCCAGATGGTCATATATTTTTAGAGA
CATTTTCAGCAATTTATAAACAAGCATCAGATTTTTTAGTTGCAATTGCA
GAACCAGTTTGTAGACCACAAAATATACATGAATATCAATTAACACCTTA
TTCATTGTATGCAGCGGTCTCTGTTGGATTAGAAACCAATGATATTATTA
CAGTTTTAGGGAGATTATCAAAATTAGCACTACCAAAAGAGGTTGAACAA
TTTGTTAGACAATGTACACAAAGTTATGGTAAAGTGAAGTTAGTATTACA
GAAGAATAAATATTTTGTGGAATCTGCATACCCAGAGGTATTGGAATTCC
Gap no gap
Contig length 600
Chromosome number (1..6, M) 3
Chromosome length 6358359
Start point 1381174
End point 1381773
Strand (PLUS/MINUS) PLUS
Number of clones 5
Number of EST 5
Link to clone list U12987
List of clone(s) 

est1=CHQ732F,1,581
est2=CHK334F,3,533
est3=AHE209F,9,600
est4=CHG470F,14,492
est5=CHM270F,28,578
Translated Amino Acid sequence 
IYKIISIMSSGDSNLKRRRGGNTGQSSKSYNTWTDYEEDLEESGEFNQSIKKTTNTSSAT
LTSSEEKGSLLDYSKRCILKQDNKSRPIWVCPDGHIFLETFSAIYKQASDFLVAIAEPVC
RPQNIHEYQLTPYSLYAAVSVGLETNDIITVLGRLSKLALPKEVEQFVRQCTQSYGKVKL
VLQKNKYFVESAYPEVLEF
Translated Amino Acid sequence (All Frames) 
Frame A:
iyik*lv*cqvvivi*reeeeeilvnhqnhiihglimkki*knlvnlinq*kkqqihqvq
h*hhqkkkdhf*iiqrgvy*nkiinqdqfgfvqmviyf*rhfqqfinkhqif*lqlqnqf
vdhkiymnin*hlihcmqrslld*kpmillqf*gdyqn*hyqkrlnnlldnvhkvmvk*s
*yyrrinilwnlhtqrywns


Frame B:
yi*nn*ynvkw***fkekkrrkywsiikii*ymd*l*rrfrriw*i*sinkknnkyikcn
iniirrkritfrlfkevyiktr**iktnlglsrwsyifrdifsnl*tsirffscncrtsl
*ttkyt*isintlfivcsglcwirnq*yyysfreiikisttkrg*tic*tmytklw*sev
sitee*ifcgiciprgigi


Frame C:
IYKIISIMSSGDSNLKRRRGGNTGQSSKSYNTWTDYEEDLEESGEFNQSIKKTTNTSSAT
LTSSEEKGSLLDYSKRCILKQDNKSRPIWVCPDGHIFLETFSAIYKQASDFLVAIAEPVC
RPQNIHEYQLTPYSLYAAVSVGLETNDIITVLGRLSKLALPKEVEQFVRQCTQSYGKVKL
VLQKNKYFVESAYPEVLEF
own update 2004. 6.10
Homology vs CSM-cDNA 
Query= Contig-U12987-1 (Contig-U12987-1Q)
/CSM_Contig/Contig-U12987-1Q.Seq.d
         (600 letters)

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


                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

Contig-U12987-1 (Contig-U12987-1Q) /CSM_Contig/Conti...  1142  0.0
Contig-U06403-1 (Contig-U06403-1Q) /CSM_Contig/Conti...    40  0.003
Contig-U14152-1 (Contig-U14152-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U02377-1 (Contig-U02377-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U02000-1 (Contig-U02000-1Q) /CSM_Contig/Conti...    36  0.042
Contig-U14699-1 (Contig-U14699-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U12483-1 (Contig-U12483-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U11685-1 (Contig-U11685-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U11342-1 (Contig-U11342-1Q) /CSM_Contig/Conti...    34  0.17
Contig-U10839-1 (Contig-U10839-1Q) /CSM_Contig/Conti...    34  0.17

>Contig-U12987-1 (Contig-U12987-1Q) /CSM_Contig/Contig-U12987-1Q.Seq.d
          Length = 600

 Score = 1142 bits (576), Expect = 0.0
 Identities = 592/600 (98%)
 Strand = Plus / Plus

                                                                       
Query: 1   atatatataaaataattagtataatgtcaagtggtgatagtaatttaaagagaagaagag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1   atatatataaaataattagtataatgtcaagtggtgatagtaatttaaagagaagaagag 60

                                                                       
Query: 61  gaggaaatactggtcaatcatcaaaatcatataatacatggactgattatgaagaagatt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61  gaggaaatactggtcaatcatcaaaatcatataatacatggactgattatgaagaagatt 120

                                                                       
Query: 121 tagaagaatctggtgaatttaatcaatcaatnnnnnnnncaacaaatacatcaagtgcaa 180
           |||||||||||||||||||||||||||||||        |||||||||||||||||||||
Sbjct: 121 tagaagaatctggtgaatttaatcaatcaataaaaaaaacaacaaatacatcaagtgcaa 180

                                                                       
Query: 181 cattaacatcatcagaagaaaaaggatcacttttagattattcaaagaggtgtatattaa 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 cattaacatcatcagaagaaaaaggatcacttttagattattcaaagaggtgtatattaa 240

                                                                       
Query: 241 aacaagataataaatcaagaccaatttgggtttgtccagatggtcatatatttttagaga 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 aacaagataataaatcaagaccaatttgggtttgtccagatggtcatatatttttagaga 300

                                                                       
Query: 301 cattttcagcaatttataaacaagcatcagattttttagttgcaattgcagaaccagttt 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 cattttcagcaatttataaacaagcatcagattttttagttgcaattgcagaaccagttt 360

                                                                       
Query: 361 gtagaccacaaaatatacatgaatatcaattaacaccttattcattgtatgcagcggtct 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 361 gtagaccacaaaatatacatgaatatcaattaacaccttattcattgtatgcagcggtct 420

                                                                       
Query: 421 ctgttggattagaaaccaatgatattattacagttttagggagattatcaaaattagcac 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 421 ctgttggattagaaaccaatgatattattacagttttagggagattatcaaaattagcac 480

                                                                       
Query: 481 taccaaaagaggttgaacaatttgttagacaatgtacacaaagttatggtaaagtgaagt 540
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 481 taccaaaagaggttgaacaatttgttagacaatgtacacaaagttatggtaaagtgaagt 540

                                                                       
Query: 541 tagtattacagaagaataaatattttgtggaatctgcatacccagaggtattggaattcc 600
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 541 tagtattacagaagaataaatattttgtggaatctgcatacccagaggtattggaattcc 600


>Contig-U06403-1 (Contig-U06403-1Q) /CSM_Contig/Contig-U06403-1Q.Seq.d
          Length = 598

 Score = 40.1 bits (20), Expect = 0.003
 Identities = 26/28 (92%)
 Strand = Plus / Plus

                                       
Query: 63  ggaaatactggtcaatcatcaaaatcat 90
           |||||||||||| ||||||||| |||||
Sbjct: 243 ggaaatactggtgaatcatcaatatcat 270


>Contig-U14152-1 (Contig-U14152-1Q) /CSM_Contig/Contig-U14152-1Q.Seq.d
          Length = 591

 Score = 36.2 bits (18), Expect = 0.042
 Identities = 18/18 (100%)
 Strand = Plus / Minus

                             
Query: 215 agattattcaaagaggtg 232
           ||||||||||||||||||
Sbjct: 424 agattattcaaagaggtg 407


  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: 8845
Number of Sequences: 6905
Number of extensions: 8845
Number of successful extensions: 980
Number of sequences better than 10.0: 124
length of query: 600
length of database: 5,674,871
effective HSP length: 16
effective length of query: 584
effective length of database: 5,564,391
effective search space: 3249604344
effective search space used: 3249604344
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 2008.12. 4
Homology vs DNA 
Query= Contig-U12987-1 (Contig-U12987-1Q) /CSM_Contig/Contig-U12987-1Q.Seq.d
         (600 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

(U77065) Dictyostelium discoideum DNA helicase homolog (repB...   866   0.0    2
(BJ332402) Dictyostelium discoideum cDNA clone:dda39a04, 5' ...   866   0.0    2
(BJ370802) Dictyostelium discoideum cDNA clone:ddc55p07, 5' ...   837   0.0    2
(BJ368421) Dictyostelium discoideum cDNA clone:ddc46k18, 5' ...   823   0.0    2
(BJ367330) Dictyostelium discoideum cDNA clone:ddc42d09, 5' ...   741   0.0    2
(BJ365246) Dictyostelium discoideum cDNA clone:ddc34l18, 5' ...   660   0.0    2
(EX615934) 255394602 Pea aphid whole body normalized full le...    54   6e-10  2
(BQ273833) rc71c05.y1 Meloidogyne hapla egg SL1 TOPO v1 Melo...    46   3e-08  3
(EX630309) 255469403 Pea aphid whole body normalized full le...    48   3e-08  2
(FC642584) CAXU607.fwd CAXU Lottia gigantea from female gona...    66   2e-06  1
(FC636024) CAXU1262.fwd CAXU Lottia gigantea from female gon...    66   2e-06  1
(FC585580) CAXP3183.fwd CAXP Lottia gigantea from head, foot...    66   2e-06  1
(EX633138) 256584047 Pea aphid whole body normalized full le...    42   7e-06  2
(FC769399) CBBN5026.fwd CBBN Lottia gigantea 3,4,5,6.5d Larv...    62   2e-05  1
(CJ397549) Molgula tectiformis cDNA, gonad clone:mtgd031j06,...    36   0.039  3
(FD524536) RUS140F07r HY Hordeum vulgare subsp. vulgare cDNA...    38   0.043  2
(FD525068) RUS118B06r HY Hordeum vulgare subsp. vulgare cDNA...    38   0.046  2
(FD525348) RUS121D08r HY Hordeum vulgare subsp. vulgare cDNA...    38   0.047  2
(AL508653) HY09G12V Hordeum vulgare cDNA clone 5'sequence; e...    38   0.047  2
(AL507772) HY06M23V Hordeum vulgare cDNA clone 5'sequence; e...    38   0.047  2
(CJ654074) Triticum aestivum cDNA clone whgc16e03 5', Y.Ogih...    38   0.049  2
(CN011786) WHE3888_G06_M12ZS Wheat Fusarium graminearum infe...    38   0.049  2
(CK161465) FGAS014035 Triticum aestivum FGAS: Library 4 Gate...    38   0.074  2
(FF773317) XABT74785.fwd Gateway compatible cien cDNA librar...    36   0.16   2
(FK148366) XABT178930.b1 Gateway compatible cien cDNA librar...    36   0.16   2
(BW319992) Ciona intestinalis cDNA, clone:cidg803c14, 5'end,...    36   0.16   2
(FF686054) XABT100360.fwd Gateway compatible cien cDNA libra...    36   0.17   2
(FK051495) XABT118770.b1 Gateway compatible cien cDNA librar...    36   0.17   2
(FF753923) XABT61553.fwd Gateway compatible cien cDNA librar...    36   0.17   2
(FK101567) XABT149355.b1 Gateway compatible cien cDNA librar...    36   0.17   2
(FF764430) XABT69024.fwd Gateway compatible cien cDNA librar...    36   0.18   2
(FK165882) XABT189904.b1 Gateway compatible cien cDNA librar...    36   0.18   2
(DR530488) WS02732.C21_L10 SS-IL-A-FL-14 Picea sitchensis cD...    34   0.19   3
(DR512291) WS02732.CR_L10 SS-IL-A-FL-14 Picea sitchensis cDN...    34   0.22   3
(EF087228) Picea sitchensis clone WS02732_L10 unknown mRNA.        34   0.27   2
(DR521770) WS0271.B21_O13 SS-IL-A-FL-14 Picea sitchensis cDN...    34   0.27   2
(AE014820) Plasmodium falciparum 3D7 chromosome 14 section 5...    48   0.36   1
(AC096534) Homo sapiens chromosome 1 clone RP11-32I17, compl...    48   0.36   1
(AC026025) Homo sapiens chromosome 1 clone CTD-2010E4, WORKI...    48   0.36   1
(AL390054) Human DNA sequence *** SEQUENCING CANCELLED *** f...    48   0.36   1
(CJ392871) Molgula tectiformis cDNA, gonad clone:mtgd007m09,...    38   0.41   2
(AP008207) Oryza sativa (japonica cultivar-group) genomic DN...    32   0.53   2
(AP003450) Oryza sativa Japonica Group genomic DNA, chromoso...    32   0.77   2
(AK103297) Oryza sativa Japonica Group cDNA clone:J033125B04...    32   0.95   2
(CT854297) Oryza sativa Indica Group EST sequence:OSIGCRA203...    32   0.98   2
(EA705497) Sequence 84376 from patent US 7365185.                  32   1.0    2
(CI096675) Oryza sativa Japonica Group cDNA, clone: 019-M065...    32   1.0    2
(AQ913728) nbeb0044D21f CUGI Rice BAC Library (EcoRI) Oryza ...    32   1.0    2
(CU019565) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f...    34   1.4    5
(BX511120) Zebrafish DNA sequence from clone CH211-214C7 in ...    46   1.4    1
(AC175374) Colobus guereza clone CH272-447L9, WORKING DRAFT ...    46   1.4    1
(AC174628) Colobus guereza clone CH272-416D24, WORKING DRAFT...    46   1.4    1
(CT720401) Danio rerio EST, clone ZF_mu_294b19 3'.                 36   1.8    2
(AC201511) Strongylocentrotus purpuratus clone R3-3084H3, WO...    44   1.8    5
(AC154755) Mus musculus BAC clone RP24-406B22 from chromosom...    38   1.9    4
(CJ391166) Molgula tectiformis cDNA, gonad clone:mtgd015o13,...    36   2.1    2
(CJ351109) Molgula tectiformis cDNA, cleaving embryo clone:m...    36   2.3    2
(CJ352785) Molgula tectiformis cDNA, cleaving embryo clone:m...    36   2.4    2
(CJ353004) Molgula tectiformis cDNA, cleaving embryo clone:m...    36   2.4    2
(CJ351290) Molgula tectiformis cDNA, cleaving embryo clone:m...    36   2.4    2
(AC116960) Dictyostelium discoideum chromosome 2 map complem...    34   2.5    7
(CU024896) M.truncatula DNA sequence from clone MTH2-150P22 ...    34   2.6    6
(EH781984) CNSS20822.b1_K21.ab1 CNS(LMS) yellow starthistle ...    36   2.7    2
(CU915601) M.truncatula DNA sequence *** SEQUENCING CANCELLE...    34   2.8    5
(DW152467) CLVX432.b1_O11.ab1 CLV(XYZ) lettuce virosa Lactuc...    42   3.0    2
(AC147201) Medicago truncatula clone mth2-117n1, complete se...    34   3.0    6
(DW160513) CLVY12587.b1_F04.ab1 CLV(XYZ) lettuce virosa Lact...    42   3.1    2
(DW160346) CLVY12426.b1_D11.ab1 CLV(XYZ) lettuce virosa Lact...    42   3.1    2
(EJ283014) 1095368002846 Global-Ocean-Sampling_GS-27-01-01-1...    40   3.1    2
(EK289871) 1095462326931 Global-Ocean-Sampling_GS-31-01-01-1...    38   3.2    2
(AL360354) Plasmodium vivax telomeric YAC clone, complete fi...    36   3.6    6
(AC025807) Homo sapiens clone RP11-657G2, WORKING DRAFT SEQU...    34   4.0    6
(EK338125) 1095467050081 Global-Ocean-Sampling_GS-31-01-01-1...    34   4.2    3
(AC115604) Dictyostelium discoideum chromosome 2 map 4354771...    36   4.5    4
(BX957305) Zebrafish DNA sequence from clone DKEYP-11G8 in l...    44   5.7    1
(BX255907) Zebrafish DNA sequence from clone DKEY-4P13 in li...    44   5.7    1
(AL844145) Mouse DNA sequence from clone RP23-403F4 on chrom...    44   5.7    1
(CR936327) Medicago truncatula chromosome 5 clone mte1-68g1,...    44   5.7    1
(CR855211) Oryza sativa genomic DNA, chromosome 4, BAC clone...    44   5.7    1
(AP008210) Oryza sativa (japonica cultivar-group) genomic DN...    44   5.7    1
(AL662938) Oryza sativa genomic DNA, chromosome 4, BAC clone...    44   5.7    1
(AL512542) Oryza sativa genomic DNA, chromosome 4, BAC clone...    44   5.7    1
(AK067292) Oryza sativa Japonica Group cDNA clone:J013105J09...    44   5.7    1
(AJ966572) Medicago sativa subsp. x varia mRNA for putative ...    44   5.7    1
(AF498359) Medicago truncatula small G-protein ROP9 mRNA, co...    44   5.7    1
(AC007069) Arabidopsis thaliana chromosome 2 clone T23K3 map...    44   5.7    1
(EA769293) Sequence 25 from patent US 7378571.                     44   5.7    1
(EA687115) Sequence 65994 from patent US 7365185.                  44   5.7    1
(EA632713) Sequence 11592 from patent US 7365185.                  44   5.7    1
(EA427602) Sequence 77 from patent US 7332281.                     44   5.7    1
(DL007621) NOVEL THERAPEUTIC TARGETS IN CANCER.                    44   5.7    1
(CS375865) Sequence 25 from Patent WO2006034479.                   44   5.7    1
(CS026517) Sequence 69 from Patent WO2005014828.                   44   5.7    1
(CQ584840) Sequence 12598 from Patent WO0171042.                   44   5.7    1
(AR833111) Sequence 13 from patent US 7026530.                     44   5.7    1
(AC160641) Ornithorhynchus anatinus BAC clone OABb-469P24 fr...    44   5.7    1
(AE014134) Drosophila melanogaster chromosome 2L, complete s...    44   5.7    1
(AC185336) Nasonia vitripennis  BAC NV_Bb-46A3 (Clemson Univ...    44   5.7    1
(AC018484) Drosophila melanogaster clone BACR13A13, complete...    44   5.7    1
(AC013351) Drosophila melanogaster clone BACR06H06, complete...    44   5.7    1

>(U77065) Dictyostelium discoideum DNA helicase homolog (repB) gene,
            complete cds.
          Length = 3093

 Score =  866 bits (437), Expect(2) = 0.0
 Identities = 440/441 (99%)
 Strand = Plus / Plus


Query: 160  caacaaatacatcaagtgcaacattaacatcatcagaagaaaaaggatcacttttagatt 219
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 601  caacaaatacatcaagtgcaacattaacatcatcagaagaaaaaggatcacttttagatt 660


Query: 220  attcaaagaggtgtatattaaaacaagataataaatcaagaccaatttgggtttgtccag 279
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 661  attcaaagaggtgtatattaaaacaagataataaatcaagaccaatttgggtttgtccag 720


Query: 280  atggtcatatatttttagagacattttcagcaatttataaacaagcatcagattttttag 339
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 721  atggtcatatatttttagagacattttcagcaatttataaacaagcatcagattttttag 780


Query: 340  ttgcaattgcagaaccagtttgtagaccacaaaatatacatgaatatcaattaacacctt 399
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 781  ttgcaattgcagaaccagtttgtagaccacaaaatatacatgaatatcaattaacacctt 840


Query: 400  attcattgtatgcagcggtctctgttggattagaaaccaatgatattattacagttttag 459
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 841  attcattgtatgcagcggtctctgttggattagaaaccaatgatattattacagttttag 900


Query: 460  ggagattatcaaaattagcactaccaaaagaggttgaacaatttgttagacaatgtacac 519
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 901  ggagattatcaaaattagcactaccaaaagaggttgaacaatttgttagacaatgtacac 960


Query: 520  aaagttatggtaaagtgaagttagtattacagaagaataaatattttgtggaatctgcat 579
            ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 961  aaagttatggtaaagtgaagttagtattacaaaagaataaatattttgtggaatctgcat 1020


Query: 580  acccagaggtattggaattcc 600
            |||||||||||||||||||||
Sbjct: 1021 acccagaggtattggaattcc 1041

 Score =  291 bits (147), Expect(2) = 0.0
 Identities = 147/147 (100%)
 Strand = Plus / Plus


Query: 1   atatatataaaataattagtataatgtcaagtggtgatagtaatttaaagagaagaagag 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 267 atatatataaaataattagtataatgtcaagtggtgatagtaatttaaagagaagaagag 326


Query: 61  gaggaaatactggtcaatcatcaaaatcatataatacatggactgattatgaagaagatt 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 327 gaggaaatactggtcaatcatcaaaatcatataatacatggactgattatgaagaagatt 386


Query: 121 tagaagaatctggtgaatttaatcaat 147
           |||||||||||||||||||||||||||
Sbjct: 387 tagaagaatctggtgaatttaatcaat 413

Lambda     K      H
    1.37    0.711     1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 828,934,231
Number of extensions: 51688025
Number of successful extensions: 4456657
Number of sequences better than 10.0: 173
Length of query: 600
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 577
Effective length of database: 93,106,754,628
Effective search space: 53722597420356
Effective search space used: 53722597420356
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)
protein update 2009. 7. 5
Homology vs Protein 
Query= Contig-U12987-1 (Contig-U12987-1Q) /CSM_Contig/Contig-U12987-1Q.Seq.d
         (600 letters)

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

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

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(O00835) RecName: Full=TFIIH basal transcription factor complex ...   360   1e-98
BC129780_1(BC129780|pid:none) Xenopus laevis hypothetical protei...   184   2e-45
(Q38861) RecName: Full=DNA repair helicase XPB1;          EC=3.6...   182   5e-45
Y17148_1(Y17148|pid:none) Geodia cydonium mRNA for XPB/ERCC-3-li...   181   1e-44
AB006707_7(AB006707|pid:none) Arabidopsis thaliana genomic DNA, ...   178   9e-44
EF676215_1(EF676215|pid:none) Picea sitchensis clone WS0271_O13 ...   177   2e-43
(Q02870) RecName: Full=DNA excision repair protein haywire;     ...   176   6e-43
(Q9FUG4) RecName: Full=DNA repair helicase XPB2;          EC=3.6...   176   6e-43
AY051975_1(AY051975|pid:none) Drosophila melanogaster LD44022 fu...   176   6e-43
A44223(A44223;S26719)DNA excision repair cross-complementing pro...   176   6e-43
T31655(T31655) DNA excision repair cross-complementing protein -...   175   8e-43
EF030553_1(EF030553|pid:none) Cricetulus griseus DNA helicase (E...   174   2e-42
(P49135) RecName: Full=TFIIH basal transcription factor complex ...   174   2e-42
AB006707_6(AB006707|pid:none) Arabidopsis thaliana genomic DNA, ...   174   2e-42
AY892340_1(AY892340|pid:none) Synthetic construct Homo sapiens c...   174   2e-42
AK222465_1(AK222465|pid:none) Homo sapiens mRNA for excision rep...   174   2e-42
AP008207_2204(AP008207|pid:none) Oryza sativa (japonica cultivar...   173   3e-42
CR954203_411(CR954203|pid:none) Ostreococcus tauri strain OTTH05...   169   5e-41
AK095557_1(AK095557|pid:none) Homo sapiens cDNA FLJ38238 fis, cl...   169   5e-41
CP000583_416(CP000583|pid:none) Ostreococcus lucimarinus CCE9901...   167   2e-40
CP001574_610(CP001574|pid:none) Micromonas sp. RCC299 chromosome...   166   5e-40
FN357594_10(FN357594|pid:none) Schistosoma mansoni genome sequen...   154   1e-36
(O13768) RecName: Full=Probable DNA repair helicase ercc3;      ...   149   6e-35
FM992695_260(FM992695|pid:none) Candida dubliniensis CD36 chromo...   148   1e-34
CU928179_600(CU928179|pid:none) Zygosaccharomyces rouxii strain ...   146   4e-34
L01414_1(L01414|pid:none) Saccharomyces cerevisiae DNA helicase ...   144   1e-33
CR382137_378(CR382137|pid:none) Debaryomyces hansenii strain CBS...   144   1e-33
AL391737_105(AL391737|pid:none) chromosome I of strain GB-M1 of ...   141   2e-32
AM910988_221(AM910988|pid:none) Plasmodium knowlesi strain H chr...   136   4e-31
AY548884_3(AY548884|pid:none) Antonospora locustae chromosome se...   132   7e-30
AM920436_1609(AM920436|pid:none) Penicillium chrysogenum Wiscons...   132   7e-30
AK300250_1(AK300250|pid:none) Homo sapiens cDNA FLJ59006 complet...   129   5e-29
AP007162_442(AP007162|pid:none) Aspergillus oryzae RIB40 genomic...   129   6e-29
AM270206_31(AM270206|pid:none) Aspergillus niger contig An09c017...   128   1e-28
CP000232_1877(CP000232|pid:none) Moorella thermoacetica ATCC 390...    73   5e-12
AM494969_415(AM494969|pid:none) Leishmania braziliensis chromoso...    64   2e-09
CP000777_2404(CP000777|pid:none) Leptospira biflexa serovar Pato...    59   1e-07
AE010300_2128(AE010300|pid:none) Leptospira interrogans serovar ...    59   1e-07
CT005269_408(CT005269|pid:none) Leishmania major strain Friedlin...    57   3e-07
AP008955_4044(AP008955|pid:none) Brevibacillus brevis NBRC 10059...    57   5e-07
AM502250_444(AM502250|pid:none) Leishmania infantum chromosome 32.     54   3e-06
AE000520_376(AE000520|pid:none) Treponema pallidum subsp. pallid...    54   4e-06
BA000035_889(BA000035|pid:none) Corynebacterium efficiens YS-314...    52   2e-05
CP001601_751(CP001601|pid:none) Corynebacterium aurimucosum ATCC...    50   6e-05
AC093543_1(AC093543|pid:none) Trypanosoma brucei chromosome 3 cl...    48   2e-04
CP001341_897(CP001341|pid:none) Arthrobacter chlorophenolicus A6...    47   5e-04
AM942444_1574(AM942444|pid:none) Corynebacterium urealyticum DSM...    45   0.001
AM942444_1570(AM942444|pid:none) Corynebacterium urealyticum DSM...    45   0.001
CP000249_4351(CP000249|pid:none) Frankia sp. CcI3, complete geno...    45   0.002
CP000431_4896(CP000431|pid:none) Rhodococcus jostii RHA1, comple...    44   0.004
CP000384_4467(CP000384|pid:none) Mycobacterium sp. MCS, complete...    43   0.006
BX248356_51(BX248356|pid:none) Corynebacterium diphtheriae gravi...    43   0.006
AP006618_635(AP006618|pid:none) Nocardia farcinica IFM 10152 DNA...    43   0.008
CP000750_3583(CP000750|pid:none) Kineococcus radiotolerans SRS30...    42   0.010
CU458896_851(CU458896|pid:none) Mycobacterium abscessus chromoso...    42   0.010
CP000656_1683(CP000656|pid:none) Mycobacterium gilvum PYR-GCK, c...    42   0.013
AL583924_195(AL583924|pid:none) Mycobacterium leprae strain TN c...    41   0.022
CP000080_58(CP000080|pid:none) Leishmania major strain Friedlin ...    41   0.022
AM408590_915(AM408590|pid:none) Mycobacterium bovis BCG Pasteur ...    41   0.029
CP000509_3894(CP000509|pid:none) Nocardioides sp. JS614, complet...    41   0.029
CT573213_6543(CT573213|pid:none) Frankia alni str. ACN14A chromo...    40   0.038
AM420293_536(AM420293|pid:none) Saccharopolyspora erythraea NRRL...    40   0.065
CP000910_479(CP000910|pid:none) Renibacterium salmoninarum ATCC ...    39   0.084
CP000850_4186(CP000850|pid:none) Salinispora arenicola CNS-205, ...    39   0.11
BA000030_3919(BA000030|pid:none) Streptomyces avermitilis MA-468...    39   0.14
AP009493_3186(AP009493|pid:none) Streptomyces griseus subsp. gri...    39   0.14
CP000325_244(CP000325|pid:none) Mycobacterium ulcerans Agy99, co...    38   0.19
CP001229_1540(CP001229|pid:none) Sulfurihydrogenibium azorense A...    36   0.71
CP000781_3288(CP000781|pid:none) Xanthobacter autotrophicus Py2,...    33   4.6
(Q3KJ97) RecName: Full=Uroporphyrinogen decarboxylase;          ...    33   7.9
CR522870_987(CR522870|pid:none) Desulfotalea psychrophila LSv54 ...    33   7.9

>(O00835) RecName: Full=TFIIH basal transcription factor complex
           helicase repB subunit;          EC=3.6.1.-; AltName:
           Full=DNA excision repair cross-complementing protein-3
           homolog; AltName: Full=DNA repair helicase repB;
           AltName: Full=DNA repair protein B;
           &U77065_1(U77065|pid:none)
          Length = 800

 Score =  360 bits (925), Expect = 1e-98
 Identities = 180/192 (93%), Positives = 180/192 (93%)
 Frame = +3

Query: 24  MSSGDSNLKRRRGGNTGQSSKSYNTWTDYEEDLEESGEFNQSIKKXXXXXXXXXXXXEEK 203
           MSSGDSNLKRRRGGNTGQSSKSYNTWTDYEEDLEESGEFNQSIKK            EEK
Sbjct: 1   MSSGDSNLKRRRGGNTGQSSKSYNTWTDYEEDLEESGEFNQSIKKTTNTSSATLTSSEEK 60

Query: 204 GSLLDYSKRCILKQDNKSRPIWVCPDGHIFLETFSAIYKQASDFLVAIAEPVCRPQNIHE 383
           GSLLDYSKRCILKQDNKSRPIWVCPDGHIFLETFSAIYKQASDFLVAIAEPVCRPQNIHE
Sbjct: 61  GSLLDYSKRCILKQDNKSRPIWVCPDGHIFLETFSAIYKQASDFLVAIAEPVCRPQNIHE 120

Query: 384 YQLTPYSLYAAVSVGLETNDIITVLGRLSKLALPKEVEQFVRQCTQSYGKVKLVLQKNKY 563
           YQLTPYSLYAAVSVGLETNDIITVLGRLSKLALPKEVEQFVRQCTQSYGKVKLVLQKNKY
Sbjct: 121 YQLTPYSLYAAVSVGLETNDIITVLGRLSKLALPKEVEQFVRQCTQSYGKVKLVLQKNKY 180

Query: 564 FVESAYPEVLEF 599
           FVESAYPEVLEF
Sbjct: 181 FVESAYPEVLEF 192

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: 823,730,129
Number of extensions: 15664327
Number of successful extensions: 32776
Number of sequences better than 10.0: 71
Number of HSP's gapped: 32758
Number of HSP's successfully gapped: 71
Length of query: 200
Length of database: 1,051,180,864
Length adjustment: 122
Effective length of query: 78
Effective length of database: 656,320,666
Effective search space: 51193011948
Effective search space used: 51193011948
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: 0.92  gvh: 0.36  alm: 0.43  top: 0.60  tms: 0.00  mit: 0.36  mip: 0.04
 nuc: 0.04  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 

	 36.0 %: cytoplasmic
	 24.0 %: mitochondrial
	 24.0 %: nuclear
	  8.0 %: cytoskeletal
	  4.0 %: plasma membrane
	  4.0 %: peroxisomal

>> prediction for Contig-U12987-1 is cyt
VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 1
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 4
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0