Contig-U04940-1
Contig ID Contig-U04940-1
Contig update 2001. 8.29
Contig sequence
>Contig-U04940-1 (Contig-U04940-1Q) /CSM_Contig/Contig-U04940-1Q.Seq.d
CATATTTATATAAACTTGTAGTAATATTGCAATCTCAAGATTCTTTCATA
TACCTGGCATTGTTCATTTCCTTTTAATAGATAGAGCTAATCATCGTATA
AGAGCACCTGTAATATCCCCAGATTTAATACCATTCCAAAGAAATAATAA
AAATAATCCTATGAATATGAGTTTTAATTTAGGTTCTGATAGTTATAATA
ATAGCAACAACAACCACAACAACAACAATCATTATCAAGGTAATAATGTT
GGTGGTATCAATTTCGATAGTATCAATATTAATATAGATCCAAATAATGA
ACAATCAATTTCAGATACTCAAAAATGGTATGGTTAGATTTTTAAAGAAA
AAGATTTGGACAATGTACAGTTATTGCTGTCAACAGTTATGTCGTGGTAA
TCATTATATGATTNGGAATGATAAAGATTTTCAATACAGTTATAGACTTT
GGATTGCCGATGATGAAAATAATGAACATAAGTTGGACCATTCCGTATCA
TTAAGATTAAATCAAAAATCATTTTATGCTGACCTTTTAAAAAATTCTTT
CCCTCATTCTTCAAAAATGAAATGTTATGAACTATTAATCCTTTANATCG
GTGTTTTACCAATNTCAATGGTTTCAAAGAATGATAAAGCATTATATCAT
TTATTATTTGAAATGGATGAATAATAACATTTTTTTTTTTAAAAAAAATT
CTGGAAATAATATTATTTTNTCAATCAAAACAAAATAAAAAAAAAAAAAA
AAACTTTTAATAAAATTAATCTTTAA

Gap no gap
Contig length 776
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 4110900
End point 4111607
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U04940
List of clone(s)

est1=SSE113E,1,777
Translated Amino Acid sequence
ylyklvvilqsqdsfiylalfisf**ieliiv*ehl*ypqi*yhskeiikiil*i*vli*
vliviiiatttttttiiikvimlvvsisivsili*IQIMNNQFQILKNGMVRFLKKKIWT
MYSYCCQQLCRGNHYMIXNDKDFQYSYRLWIADDENNEHKLDHSVSLRLNQKSFYADLLK
NSFPHSSKMKCYELLILXIGVLPXSMVSKNDKALYHLLFEMDE**hfff*kkfwk*yyfx
nqnkikkkkktfnkinl*


Translated Amino Acid sequence (All Frames)
Frame A:
hiyinl**ycnlkilsytwhcsfpfnr*s*ssykstcniprfntipkk**k*syeyef*f
rf**l***qqqpqqqqslsr**cwwyqfr*yqy*yrsk**tinfryskmvwldf*rkrfg
qctviavnsyvvviii*xgmikifntvidfglpmmkimniswtipyh*d*iknhfmltf*
kilslilqk*nvmny*sfxsvfyqxqwfqrmikhyiiyylkwmnnnifffkknsgnniix
siktk*kkkkklliklif


Frame B:
ifi*tcsniaisrffhipgivhfllidranhrirapvispdlipfqrnnknnpmnmsfnl
gsdsynnsnnnhnnnnhyqgnnvgginfdsininidpnneqsisdtqkwyg*ifkekdld
nvqlllstvmsw*slydxe**rfsiql*tldcr**k**t*vgpfriikikskiilc*pfk
kffpsffkneml*tinplxrcftnxngfke**siisfii*ng*iitffflkkileiilfx
qskqnkkkkknf**n*sl


Frame C:
ylyklvvilqsqdsfiylalfisf**ieliiv*ehl*ypqi*yhskeiikiil*i*vli*
vliviiiatttttttiiikvimlvvsisivsili*IQIMNNQFQILKNGMVRFLKKKIWT
MYSYCCQQLCRGNHYMIXNDKDFQYSYRLWIADDENNEHKLDHSVSLRLNQKSFYADLLK
NSFPHSSKMKCYELLILXIGVLPXSMVSKNDKALYHLLFEMDE**hfff*kkfwk*yyfx
nqnkikkkkktfnkinl*


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U04940-1 (Contig-U04940-1Q)
/CSM_Contig/Contig-U04940-1Q.Seq.d
(776 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U04940-1 (Contig-U04940-1Q) /CSM_Contig/Conti... 918 0.0
Contig-U12243-1 (Contig-U12243-1Q) /CSM_Contig/Conti... 52 9e-07
Contig-U01501-1 (Contig-U01501-1Q) /CSM_Contig/Conti... 40 0.003
Contig-U05451-1 (Contig-U05451-1Q) /CSM_Contig/Conti... 38 0.014
Contig-U12899-1 (Contig-U12899-1Q) /CSM_Contig/Conti... 36 0.054
Contig-U11921-1 (Contig-U11921-1Q) /CSM_Contig/Conti... 36 0.054
Contig-U11513-1 (Contig-U11513-1Q) /CSM_Contig/Conti... 36 0.054
Contig-U11196-1 (Contig-U11196-1Q) /CSM_Contig/Conti... 36 0.054
Contig-U14636-1 (Contig-U14636-1Q) /CSM_Contig/Conti... 34 0.22
Contig-U14359-1 (Contig-U14359-1Q) /CSM_Contig/Conti... 34 0.22

>Contig-U04940-1 (Contig-U04940-1Q) /CSM_Contig/Contig-U04940-1Q.Seq.d
Length = 776

Score = 918 bits (463), Expect = 0.0
Identities = 497/508 (97%)
Strand = Plus / Plus


Query: 229 tcattatcaaggtaataatgttggtggtatcaatttcgatagtatcaatattaatataga 288
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 229 tcattatcaaggtaataatgttggtggtatcaatttcgatagtatcaatattaatataga 288


Query: 289 tccaaataatgaacaatcaatttcagatactcaaaaatggtatggttagatttttaaaga 348
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 289 tccaaataatgaacaatcaatttcagatactcaaaaatggtatggttagatttttaaaga 348


Query: 349 aaaagatttggacaatgtacagttattgctgtcaacagttatgtcgtggtaatcattata 408
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 349 aaaagatttggacaatgtacagttattgctgtcaacagttatgtcgtggtaatcattata 408


Query: 409 tgattnggaatgataaagattttcaatacagttatagactttggattgccgatgatgaaa 468
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 409 tgattnggaatgataaagattttcaatacagttatagactttggattgccgatgatgaaa 468


Query: 469 ataatgaacataagttggaccattccgtatcattaagattaaatcaaaaatcattttatg 528
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 469 ataatgaacataagttggaccattccgtatcattaagattaaatcaaaaatcattttatg 528


Query: 529 ctgaccttttaaaaaattctttccctcattcttcaaaaatgaaatgttatgaactattaa 588
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 529 ctgaccttttaaaaaattctttccctcattcttcaaaaatgaaatgttatgaactattaa 588


Query: 589 tcctttanatcggtgttttaccaatntcaatggtttcaaagaatgataaagcattatatc 648
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 589 tcctttanatcggtgttttaccaatntcaatggtttcaaagaatgataaagcattatatc 648


Query: 649 atttattatttgaaatggatgaataataacannnnnnnnnnnaaaaaaaattctggaaat 708
||||||||||||||||||||||||||||||| ||||||||||||||||||
Sbjct: 649 atttattatttgaaatggatgaataataacatttttttttttaaaaaaaattctggaaat 708


Query: 709 aatattattttntcaatcaaaacaaaat 736
||||||||||||||||||||||||||||
Sbjct: 709 aatattattttntcaatcaaaacaaaat 736


Score = 404 bits (204), Expect = e-113
Identities = 204/204 (100%)
Strand = Plus / Plus


Query: 1 catatttatataaacttgtagtaatattgcaatctcaagattctttcatatacctggcat 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 catatttatataaacttgtagtaatattgcaatctcaagattctttcatatacctggcat 60


Query: 61 tgttcatttccttttaatagatagagctaatcatcgtataagagcacctgtaatatcccc 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 tgttcatttccttttaatagatagagctaatcatcgtataagagcacctgtaatatcccc 120


Query: 121 agatttaataccattccaaagaaataataaaaataatcctatgaatatgagttttaattt 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 agatttaataccattccaaagaaataataaaaataatcctatgaatatgagttttaattt 180


Query: 181 aggttctgatagttataataatag 204
||||||||||||||||||||||||
Sbjct: 181 aggttctgatagttataataatag 204


Score = 46.1 bits (23), Expect = 6e-05
Identities = 23/23 (100%)
Strand = Plus / Plus


Query: 754 cttttaataaaattaatctttaa 776
|||||||||||||||||||||||
Sbjct: 754 cttttaataaaattaatctttaa 776


>Contig-U12243-1 (Contig-U12243-1Q) /CSM_Contig/Contig-U12243-1Q.Seq.d
Length = 1637

Score = 52.0 bits (26), Expect = 9e-07
Identities = 26/26 (100%)
Strand = Plus / Plus


Query: 1 catatttatataaacttgtagtaata 26
||||||||||||||||||||||||||
Sbjct: 704 catatttatataaacttgtagtaata 729


>Contig-U01501-1 (Contig-U01501-1Q) /CSM_Contig/Contig-U01501-1Q.Seq.d
Length = 1233

Score = 40.1 bits (20), Expect = 0.003
Identities = 23/24 (95%)
Strand = Plus / Plus


Query: 622 tttcaaagaatgataaagcattat 645
|||||||||||||||||| |||||
Sbjct: 501 tttcaaagaatgataaagaattat 524


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: 18,673
Number of Sequences: 6905
Number of extensions: 18673
Number of successful extensions: 2295
Number of sequences better than 10.0: 447
length of query: 776
length of database: 5,674,871
effective HSP length: 16
effective length of query: 760
effective length of database: 5,564,391
effective search space: 4228937160
effective search space used: 4228937160
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. 7. 5
Homology vs DNA
Query= Contig-U04940-1 (Contig-U04940-1Q) /CSM_Contig/Contig-U04940-1Q.Seq.d
(776 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

(AU037636) Dictyostelium discoideum slug cDNA, clone SSE113. 692 0.0 3
(AU072288) Dictyostelium discoideum slug cDNA, clone SSE113. 404 e-108 1
(AE013218) Buchnera aphidicola str. Sg (Schizaphis graminum)... 38 0.012 12
(AL844506) Plasmodium falciparum chromosome 7. 40 0.023 15
(C93361) Dictyostelium discoideum slug cDNA, clone SSM671. 52 0.032 1
(C90802) Dictyostelium discoideum slug cDNA, clone SSJ166. 52 0.032 1
(BJ411840) Dictyostelium discoideum cDNA clone:ddv6c03, 5' e... 52 0.032 1
(AC116982) Dictyostelium discoideum chromosome 2 map 3622643... 32 0.081 12
(GE806545) EST_scau_evk_971547 scauevk mixed_tissue Sebastes... 40 0.092 2
(EW978238) EST_sras_evg_777463 srasevg mixed_tissue Sebastes... 40 0.093 2
(EW984986) EST_sras_evg_777879 srasevg mixed_tissue Sebastes... 40 0.095 2
(EW985351) EST_sras_evg_778065 srasevg mixed_tissue Sebastes... 40 0.096 2
(AC116305) Dictyostelium discoideum chromosome 2 map 1005175... 40 0.16 11
(CP000721) Clostridium beijerinckii NCIMB 8052, complete gen... 34 0.18 16
(CP000942) Ureaplasma parvum serovar 3 str. ATCC 27815, comp... 32 0.20 15
(AF222894) Ureaplasma parvum serovar 3 str. ATCC 700970, com... 32 0.20 15
(CP000727) Clostridium botulinum A str. Hall, complete genome. 36 0.20 17
(AF030694) Plasmodium falciparum strain Dd2 heat shock prote... 40 0.22 7
(AE014821) Plasmodium falciparum 3D7 chromosome 14 section 6... 32 0.26 11
(CP000726) Clostridium botulinum A str. ATCC 19397, complete... 36 0.27 17
(AM412317) Clostridium botulinum A str. ATCC 3502 complete g... 36 0.28 17
(DQ198583) Phengodes sp. UPOL 000M29 cytochrome oxidase subu... 48 0.51 1
(BX664703) Zebrafish DNA sequence from clone DKEYP-74A8 in l... 38 0.58 7
(AE014828) Plasmodium falciparum 3D7 chromosome 14 section 1... 32 0.65 13
(AC115592) Dictyostelium discoideum chromosome 2 map 1-12595... 32 0.67 6
(CP000395) Borrelia afzelii PKo, complete genome. 36 0.95 14
(U89350) Dictyostelium discoideum golvesin (gol) gene, compl... 42 1.0 2
(AC133822) Rattus norvegicus clone CH230-235C5, *** SEQUENCI... 32 1.0 2
(AC110433) Rattus norvegicus clone CH230-230O15, WORKING DRA... 32 1.0 2
(AC083817) Mus musculus 1 BAC RP23-470G12 (Roswell Park Canc... 38 1.2 3
(CP000123) Mycoplasma capricolum subsp. capricolum ATCC 2734... 38 1.5 17
(AL049184) Plasmodium falciparum DNA *** SEQUENCING IN PROGR... 32 1.5 10
(AC140024) Medicago truncatula chromosome 8 clone mth2-5f21,... 44 1.8 4
(AE014834) Plasmodium falciparum 3D7 chromosome 10 section 6... 34 1.9 7
(AF295546) Malawimonas jakobiformis mitochondrial DNA, compl... 36 2.0 5
(BX005316) Zebrafish DNA sequence from clone CH211-287H3. 46 2.0 1
(AL929392) Zebrafish DNA sequence from clone CH211-79L17 in ... 46 2.0 1
(AC157593) Mus musculus BAC clone RP23-254B18 from chromosom... 46 2.0 1
(AC102083) Mus musculus chromosome 16, clone RP23-269L18, co... 46 2.0 1
(AC166314) Medicago truncatula chromosome 2 BAC clone mth2-1... 46 2.0 1
(AC159835) Bos taurus clone CH240-78B22, WORKING DRAFT SEQUE... 46 2.0 1
(AC110663) Bos taurus clone RP42-343B18, WORKING DRAFT SEQUE... 46 2.0 1
(CU302261) Pig DNA sequence *** SEQUENCING IN PROGRESS *** f... 46 2.0 1
(AC220217) Bos taurus clone CH240-366J10, WORKING DRAFT SEQU... 46 2.0 1
(EJ696514) 1092956020775 Global-Ocean-Sampling_GS-30-02-01-1... 46 2.0 1
(EJ652581) 1092954006084 Global-Ocean-Sampling_GS-30-02-01-1... 46 2.0 1
(DX601158) ZMMBBc0261C14.fq ZMMBB_VAL Zea mays genomic clone... 46 2.0 1
(DU877261) 220226 Tomato HindIII BAC Library Solanum lycoper... 46 2.0 1
(DH380620) Oryzias latipes Fosmid clone:GOLWFno781_a14, forw... 46 2.0 1
(CT707260) Danio rerio EST, clone ZF_mu_200a18 3'. 46 2.0 1
(CT707259) Danio rerio EST, clone ZF_mu_200a18 5'. 46 2.0 1
(BJ731143) Oryzias latipes cDNA clone:MF015DA013o12, 5' end. 46 2.0 1
(BB202751) Mus musculus 0 day neonate thymus cDNA, RIKEN ful... 42 2.0 2
(AC167388) Bos taurus clone CH240-137P12, WORKING DRAFT SEQU... 36 2.0 5
(AL844501) Plasmodium falciparum strain 3D7, chromosome 1. 34 2.1 13
(AC073551) Homo sapiens BAC clone RP11-498C14 from 2, comple... 38 2.2 4
(AC138580) Medicago truncatula chromosome 6 clone mth2-14e15... 36 2.4 7
(DY697067) EST_ssal_rgb2_52806 ssalrgb2 mixed_tissue Salmo s... 42 2.5 2
(AC159437) Trypanosoma brucei chromosome 7 clone RPCI93-29K4... 38 2.7 3
(AC099863) Mus musculus chromosome 3, clone RP23-6F2, comple... 38 2.9 6
(AC069399) Homo sapiens chromosome 3 clone RP11-348L20 map 3... 44 2.9 4
(AC116977) Dictyostelium discoideum chromosome 2 map 5515173... 32 3.0 10
(CU463345) Mouse DNA sequence from clone RP24-346O11 on chro... 38 3.3 3
(AC202298) Medicago truncatula clone mth2-82e22, complete se... 36 3.4 5
(AF222718) Chrysodidymus synuroideus mitochondrion, complete... 32 3.4 6
(AL929356) Plasmodium falciparum strain 3D7, chromosome 9; s... 30 3.5 13
(AQ046873) RPCI11-33M20.TK RPCI-11 Homo sapiens genomic clon... 34 3.6 3
(AC117081) Dictyostelium discoideum chromosome 2 map 5862124... 34 3.6 9
(AC219450) Bos taurus clone CH240-340P12, WORKING DRAFT SEQU... 38 3.7 3
(AC094963) Rattus norvegicus X BAC CH230-6L20 (Children's Ho... 34 3.8 2
(AC116986) Dictyostelium discoideum chromosome 2 map 2234041... 40 3.8 8
(CR356240) Zebrafish DNA sequence from clone CH211-226E7 in ... 32 3.8 2
(CU464119) Zebrafish DNA sequence from clone CH73-271G12 in ... 34 3.8 5
(AC137889) Homo sapiens chromosome 8 clone RP11-164D17 map 8... 38 3.8 4
(BX247870) Zebrafish DNA sequence from clone RP71-24B12 in l... 32 3.9 2
(CU041370) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 36 3.9 3
(CP000361) Arcobacter butzleri RM4018, complete genome. 38 4.0 15
(EI520872) MUGQ_CH252P241P07Sp6_CN460_018 CHORI-252 Vervet M... 34 4.1 2
(AC092801) Homo sapiens chromosome 1 clone RP11-36N20, compl... 36 4.1 6
(AC104303) Homo sapiens chromosome 3 clone RP11-391P4, compl... 36 4.2 5
(AC149788) Pan troglodytes BAC clone CH251-63L13 from chromo... 40 4.3 4
(AE014843) Plasmodium falciparum 3D7 chromosome 11 section 8... 32 4.4 9
(AC116924) Dictyostelium discoideum chromosome 2 map 6357117... 34 4.5 5
(AF250284) Amsacta moorei entomopoxvirus, complete genome. 36 5.0 9
(AC117070) Dictyostelium discoideum chromosome 2 map 2097701... 34 5.1 9
(AC175126) Bos taurus clone CH240-459D20, WORKING DRAFT SEQU... 40 5.2 4
(CP001205) Borrelia burgdorferi ZS7, complete genome. 36 5.3 11
(AZ693037) ENTHP79TF Entamoeba histolytica Sheared DNA Entam... 40 5.3 2
(AI168538) oz42b05.s1 Soares_NhHMPu_S1 Homo sapiens cDNA clo... 34 5.6 2
(AE014847) Plasmodium falciparum 3D7 chromosome 12, section ... 34 5.6 7
(AE014842) Plasmodium falciparum 3D7 chromosome 11 section 7... 32 5.7 11
(AC149953) Strongylocentrotus purpuratus clone R3-32B17, WOR... 34 5.9 5
(EK576972) 1095521355481 Global-Ocean-Sampling_GS-32-01-01-1... 34 6.4 3
(AC178057) Strongylocentrotus purpuratus clone R3-3056G04, W... 34 6.6 7
(AM471579) Vitis vinifera contig VV78X046697.1, whole genome... 36 6.6 2
(AL589679) Mouse DNA sequence from clone RP23-189A16 on chro... 42 6.7 5
(CR376842) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 38 6.7 6
(AE014816) Plasmodium falciparum 3D7 chromosome 14 section 1... 32 6.8 10
(AE014849) Plasmodium falciparum 3D7 chromosome 12, section ... 32 6.9 10
(CT476817) Zebrafish DNA sequence from clone CH211-62C1 in l... 38 6.9 6
(DV742201) ID0AFF6BG11CM1 ID0AFF Acyrthosiphon pisum cDNA cl... 38 7.2 2
(AA259131) zs30c02.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone ... 34 7.3 3
(BH154372) ENTTH52TR Entamoeba histolytica Sheared DNA Entam... 32 7.7 3
(AA830778) oc56a10.s1 NCI_CGAP_GCB1 Homo sapiens cDNA clone ... 34 7.8 3
(BX005044) Zebrafish DNA sequence from clone DKEY-7L6 in lin... 44 7.9 1
(BV644092) S217P6990RH5.T0 Noemie Pan troglodytes troglodyte... 44 7.9 1
(AL845488) Mouse DNA sequence from clone RP23-215P8 on chrom... 44 7.9 1
(CU104666) Gorilla DNA sequence from clone CH255-415I16. 44 7.9 1
(CU104654) Gorilla DNA sequence from clone CH255-13G2. 44 7.9 1
(BA000041) Pan troglodytes DNA, major histocompatibility com... 44 7.9 1
(AC200691) MACACA MULATTA BAC clone CH250-157G13 from chromo... 44 7.9 1
(AB054536) Pan troglodytes LTB, TNF alpha, LTA, IKBL, ATP6G,... 44 7.9 1
(AY558680) Phellinus ferrugineovelutinus strain CBS 218.48 s... 44 7.9 1
(AM270350) Aspergillus niger contig An15c0230, complete genome. 44 7.9 1
(DJ008493) Methods and Compositions for Differentiating Tiss... 44 7.9 1
(CS452618) Sequence 18 from Patent WO2006119494. 44 7.9 1
(CS452617) Sequence 17 from Patent WO2006119494. 44 7.9 1
(CS039419) Sequence 229 from Patent WO2005019477. 44 7.9 1
(GC698988) Sequence 14233 from patent US 6812339. 44 7.9 1
(GC696536) Sequence 11780 from patent US 6812339. 44 7.9 1
(AR535919) Sequence 481 from patent US 6737248. 44 7.9 1
(AR354363) Sequence 481 from patent US 6593114. 44 7.9 1
(AC114263) Dictyostelium discoideum chromosome 2 map 215673-... 44 7.9 1
(X92841) H.sapiens MICA gene. 44 7.9 1
(L29411) Homo sapiens MHC class I alpha chain gene, leader e... 44 7.9 1
(D84394) Homo sapiens genomic DNA, 237 kb segment from 6p21.... 44 7.9 1
(CR847852) Human DNA sequence from clone DAMA-345G11 on chro... 44 7.9 1
(BX119958) Human DNA sequence from clone DASS-38L18 on chrom... 44 7.9 1
(BA000025) Homo sapiens genomic DNA, chromosome 6p21.3, HLA ... 44 7.9 1
(AP003486) Homo sapiens genomic DNA, chromosome 11 clone:RP1... 44 7.9 1
(AP000824) Homo sapiens genomic DNA, chromosome 11 clone:RP1... 44 7.9 1
(AL845443) Human DNA sequence from clone DAQB-48K1 on chromo... 44 7.9 1
(AL669854) Human DNA sequence from clone XXbac-25O20 on chro... 44 7.9 1
(AL645933) Human DNA sequence from clone XXbac-181B23 on chr... 44 7.9 1
(AC098677) Homo sapiens BAC clone RP11-416E16 from 4, comple... 44 7.9 1
(AC093001) Homo sapiens 3 BAC RP11-206M11 (Roswell Park Canc... 44 7.9 1
(AC066694) Homo sapiens BAC clone RP11-655A7 from 2, complet... 44 7.9 1
(AC004180) Homo sapiens clone UWGC:M32A from 6p21, complete ... 44 7.9 1
(AC129376) Rattus norvegicus clone CH230-83P17, *** SEQUENCI... 44 7.9 1
(AC126413) Mus musculus clone RP24-340A9, WORKING DRAFT SEQU... 44 7.9 1
(AC126239) Felis catus clone RP86-474H17, WORKING DRAFT SEQU... 44 7.9 1
(AC106403) Rattus norvegicus clone CH230-129B20, *** SEQUENC... 44 7.9 1
(AC091741) Homo sapiens chromosome 4 clone RP11-689E2, *** S... 44 7.9 1
(AC072027) Homo sapiens chromosome 3 clone RP11-268J1, WORKI... 44 7.9 1
(AC069268) Homo sapiens chromosome 3p clone RP11-348I20, WOR... 44 7.9 1
(AC037468) Homo sapiens chromosome 4 clone RP11-198E18 map 4... 44 7.9 1
(AC233206) Monodelphis domestica clone VMRC18-928C19, WORKIN... 44 7.9 1
(AC233017) Monodelphis domestica clone VMRC18-348E13, WORKIN... 44 7.9 1
(AC223985) Bos taurus clone CH240-452I19, WORKING DRAFT SEQU... 44 7.9 1
(AC223844) Bos taurus clone CH240-456D12, WORKING DRAFT SEQU... 44 7.9 1
(AC199665) Nomascus leucogenys leucogenys clone CH271-201N17... 44 7.9 1
(AC181722) Strongylocentrotus purpuratus clone R3-1039G04, W... 44 7.9 1
(AC178363) Strongylocentrotus purpuratus clone R3-3107B10, W... 44 7.9 1
(AC176104) Strongylocentrotus purpuratus clone R3-24F10, WOR... 44 7.9 1
(AC175945) Strongylocentrotus purpuratus clone R3-17C11, WOR... 44 7.9 1
(AC168758) Strongylocentrotus purpuratus clone R3-3004I8, WO... 44 7.9 1
(AC166956) Bos taurus clone CH240-188C18, WORKING DRAFT SEQU... 44 7.9 1
(AC163504) Bos taurus clone CH240-241B2, WORKING DRAFT SEQUE... 44 7.9 1
(AC025119) Homo sapiens chromosome 3 clone RP11-206M11 map 3... 44 7.9 1
(AC022249) Homo sapiens clone RP11-24G14, WORKING DRAFT SEQU... 44 7.9 1
(EK332474) 1095467028959 Global-Ocean-Sampling_GS-31-01-01-1... 44 7.9 1
(EK045426) 1092959547682 Global-Ocean-Sampling_GS-31-01-01-1... 44 7.9 1
(AM660931) Entamoeba moshkovskii FIC GSS, clone mosh104b01.p1k. 44 7.9 1
(AM644205) Entamoeba moshkovskii FIC GSS, clone mosh007f11.q1k. 44 7.9 1
(EI327397) GM_WBc0065F06.r GM_WBc Glycine max genomic clone ... 44 7.9 1
(DX458915) Cpl00569 Papaya Genomic DNA BAC Library Carica pa... 44 7.9 1
(BH985815) oeh96e08.b1 B.oleracea002 Brassica oleracea genom... 44 7.9 1
(EC320062) EMBRYOF088896J3 POSSUM_01-POSSUM-C-EMBRYO-2KB Tri... 44 7.9 1
(DT861718) LB00552.CR_P11 GC_BGC-05 Bos taurus cDNA clone IM... 44 7.9 1
(DN815936) ACAC-aac21c17.g1 Hydra EST UCI 7 Hydra magnipapil... 44 7.9 1
(CB987280) AGENCOURT_13643080 NIH_MGC_184 Homo sapiens cDNA ... 44 7.9 1
(EY475793) METAK22TF JCVI-MT3 Medicago truncatula cDNA 5', m... 44 7.9 1
(CP000736) Staphylococcus aureus subsp. aureus JH1, complete... 44 7.9 1
(CP000730) Staphylococcus aureus subsp. aureus USA300_TCH151... 44 7.9 1
(CP000703) Staphylococcus aureus subsp. aureus JH9, complete... 44 7.9 1
(CP000255) Staphylococcus aureus subsp. aureus USA300_FPR375... 44 7.9 1
(CP000253) Staphylococcus aureus subsp. aureus NCTC 8325, co... 44 7.9 1
(CP000046) Staphylococcus aureus subsp. aureus COL, complete... 44 7.9 1
(BA000018) Staphylococcus aureus subsp. aureus N315 DNA, com... 44 7.9 1
(BA000017) Staphylococcus aureus subsp. aureus Mu50 DNA, com... 44 7.9 1
(AP009351) Staphylococcus aureus subsp. aureus str. Newman D... 44 7.9 1
(AP009324) Staphylococcus aureus subsp. aureus Mu3 DNA, comp... 44 7.9 1
(AM398681) Flavobacterium psychrophilum JIP02/86 complete ge... 44 7.9 1
(AM260525) Bartonella tribocorum CIP 105476 complete genome,... 44 7.9 1
(AJ938182) Staphylococcus aureus RF122 complete genome. 44 7.9 1
(CU928762) Zebrafish DNA sequence from clone CH73-203I3 in l... 32 8.0 5
(AC159458) Trypanosoma brucei chromosome 7 clone RPCI93-8P12... 38 8.3 3
(AB365355) Candida boidinii TRM1 gene for Zn(II)2Cys6-type t... 30 8.7 5
(CU302254) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 36 8.8 5
(AC176307) Strongylocentrotus purpuratus clone R3-3057B1, WO... 40 9.2 7
(AE014298) Drosophila melanogaster chromosome X, complete se... 30 9.3 2
(AC127908) Rattus norvegicus clone CH230-213E7, WORKING DRAF... 36 9.8 4
(AC168488) Strongylocentrotus purpuratus clone R3-3117J19, W... 40 9.9 4

>(AU037636) Dictyostelium discoideum slug cDNA, clone SSE113.
Length = 558

Score = 692 bits (349), Expect(3) = 0.0
Identities = 358/358 (100%)
Strand = Plus / Plus


Query: 322 aaaatggtatggttagatttttaaagaaaaagatttggacaatgtacagttattgctgtc 381
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 94 aaaatggtatggttagatttttaaagaaaaagatttggacaatgtacagttattgctgtc 153


Query: 382 aacagttatgtcgtggtaatcattatatgattnggaatgataaagattttcaatacagtt 441
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 154 aacagttatgtcgtggtaatcattatatgattnggaatgataaagattttcaatacagtt 213


Query: 442 atagactttggattgccgatgatgaaaataatgaacataagttggaccattccgtatcat 501
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 214 atagactttggattgccgatgatgaaaataatgaacataagttggaccattccgtatcat 273


Query: 502 taagattaaatcaaaaatcattttatgctgaccttttaaaaaattctttccctcattctt 561
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 274 taagattaaatcaaaaatcattttatgctgaccttttaaaaaattctttccctcattctt 333


Query: 562 caaaaatgaaatgttatgaactattaatcctttanatcggtgttttaccaatntcaatgg 621
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 334 caaaaatgaaatgttatgaactattaatcctttanatcggtgttttaccaatntcaatgg 393


Query: 622 tttcaaagaatgataaagcattatatcatttattatttgaaatggatgaataataaca 679
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 394 tttcaaagaatgataaagcattatatcatttattatttgaaatggatgaataataaca 451

Score = 190 bits (96), Expect(3) = 0.0
Identities = 96/96 (100%)
Strand = Plus / Plus


Query: 229 tcattatcaaggtaataatgttggtggtatcaatttcgatagtatcaatattaatataga 288
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 2 tcattatcaaggtaataatgttggtggtatcaatttcgatagtatcaatattaatataga 61


Query: 289 tccaaataatgaacaatcaatttcagatactcaaaa 324
||||||||||||||||||||||||||||||||||||
Sbjct: 62 tccaaataatgaacaatcaatttcagatactcaaaa 97

Score = 46.1 bits (23), Expect(3) = 0.0
Identities = 23/23 (100%)
Strand = Plus / Plus


Query: 754 cttttaataaaattaatctttaa 776
|||||||||||||||||||||||
Sbjct: 526 cttttaataaaattaatctttaa 548

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 994,096,822
Number of extensions: 67811810
Number of successful extensions: 5829216
Number of sequences better than 10.0: 193
Length of query: 776
Length of database: 101,790,757,118
Length adjustment: 24
Effective length of query: 752
Effective length of database: 99,340,224,878
Effective search space: 74703849108256
Effective search space used: 74703849108256
X1: 11 (21.8 bits)
S2: 22 (44.1 bits)

protein update 2009. 7.31
Homology vs Protein
Query= Contig-U04940-1 (Contig-U04940-1Q) /CSM_Contig/Contig-U04940-1Q.Seq.d
(776 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

BC108057_1(BC108057|pid:none) Danio rerio zgc:123240, mRNA (cDNA... 51 5e-05
BX294129_2(BX294129|pid:none) Zebrafish DNA sequence from clone ... 51 5e-05
U78315_1(U78315|pid:none) Mus musculus Hermansky-Pudlak syndrome... 50 8e-05
CR860688_1(CR860688|pid:none) Pongo abelii mRNA; cDNA DKFZp459M1... 49 1e-04
AF333325_1(AF333325|pid:none) Rattus norvegicus Hermansky-Pudlak... 49 1e-04
(Q92902) RecName: Full=Hermansky-Pudlak syndrome 1 protein; &AF... 49 1e-04
BC099744_1(BC099744|pid:none) Rattus norvegicus Hermansky-Pudlak... 49 1e-04
AK171225_1(AK171225|pid:none) Mus musculus NOD-derived CD11c +ve... 49 1e-04
(Q60HF3) Hermansky-Pudlak syndrome 1 protein homolog. &AB125174... 49 1e-04
U65676_1(U65676|pid:none) Homo sapiens Hermansky-Pudlak syndrome... 49 1e-04
BT026531_1(BT026531|pid:none) Bos taurus Hermansky-Pudlak syndro... 42 0.017
BC123790_1(BC123790|pid:none) Bos taurus Hermansky-Pudlak syndro... 42 0.017
AE013599_2072(AE013599|pid:none) Drosophila melanogaster chromos... 40 0.084
CP001097_264(CP001097|pid:none) Chlorobium limicola DSM 245, com... 34 6.0
BC089331_1(BC089331|pid:none) Mus musculus Hermansky-Pudlak synd... 33 7.8

>BC108057_1(BC108057|pid:none) Danio rerio zgc:123240, mRNA (cDNA
clone MGC:123240 IMAGE:7437579), complete cds.
Length = 668

Score = 50.8 bits (120), Expect = 5e-05
Identities = 32/123 (26%), Positives = 62/123 (50%), Gaps = 9/123 (7%)
Frame = +3

Query: 321 KNGMVRFLKKKIWTMYSYCCQQLCRGNHYMIXNDKDFQYSYRLWIADDENNEHKL----- 485
K + F+KKK+W++ + + L +G + D D+ Y Y LW ++ + ++
Sbjct: 539 KGPLADFIKKKVWSLVATARRYLHKGYATVTLRDGDYFYCYFLWFENETGYKLEVTDIPS 598

Query: 486 --DHSVSLRLNQKSFYADLLK-NSFPHSSK-MKCYELLILXIGVLPXSMVSKNDKALYHL 653
D + + + +Y LL+ S H ++ +KCYELL + +GV+P + ++ L
Sbjct: 599 CPDDTAPIGMLTFDYYRKLLRYYSKKHQNEVVKCYELLTVHLGVIPNEYILQHCSQLARK 658

Query: 654 LFE 662
L+E
Sbjct: 659 LWE 661

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: 848,561,727
Number of extensions: 13208184
Number of successful extensions: 36315
Number of sequences better than 10.0: 15
Number of HSP's gapped: 36291
Number of HSP's successfully gapped: 15
Length of query: 258
Length of database: 1,061,185,681
Length adjustment: 126
Effective length of query: 132
Effective length of database: 649,361,233
Effective search space: 85715682756
Effective search space used: 85715682756
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: 31 (16.5 bits)

PSORT

psg: 0.71 gvh: 0.40 alm: 0.34 top: 0.53 tms: 0.00 mit: 0.36 mip: 0.07
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

32.0 %: cytoplasmic
32.0 %: mitochondrial
32.0 %: nuclear
4.0 %: cytoskeletal

>> prediction for Contig-U04940-1 is cyt

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) 1
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