Contig-U06349-1
Contig ID Contig-U06349-1
Contig update 2002. 9.13
Contig sequence
>Contig-U06349-1 (Contig-U06349-1Q) /CSM_Contig/Contig-U06349-1Q.Seq.d
TGGTGATGAATTTTTAATCATTAAAAGAGGTGTTGAAAATGTTGATCATG
CTGATCATTTCATTTCACAATTCACTAAAAACGTCTCTTCAAGTAGCTTC
ACTGTCGACGGTGAATCAAGTTCAACCATTTTTCCAATTTTCTTTTCANA
TGGTGGTGTTGTCTTTAAAAAATNTGAAACTAAAGTTTCTTCAATTATTA
AATCTGCCGATGNAAAAATGTATCAAATGGAAAAAGGNATTAGTCAAATA
AATGTTGTTGAATTTGNAAAAAATTAAATTCAATTTTAAANATATAAANA
TATATTTTTTTTTTAAAAAAAAAAAAAAAAAGNAAAAAAAAAAAAAAAAA
AAAAGAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAATT
AAATAAATACATAAATAAAAAAAAAATGATTATAAAAAAAAAAA

Gap no gap
Contig length 444
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 719249
End point 718805
Strand (PLUS/MINUS) MINUS
Number of clones 1
Number of EST 1
Link to clone list U06349
List of clone(s)

est1=VSB305Z,1,445
Translated Amino Acid sequence
GDEFLIIKRGVENVDHADHFISQFTKNVSSSSFTVDGESSSTIFPIFFSXGGVVFKKXET
KVSSIIKSADXKMYQMEKGISQINVVEFXKN*iqf*xykxifff*kkkkkxkkkkkkkkk
kkkkkkkkkkkkik*ihk*kkndykkk


Translated Amino Acid sequence (All Frames)
Frame A:
w**ifnh*krc*kc*sc*sfhftih*krlfk*lhcrr*ikfnhfsnflfxwwccl*kx*n
*sffny*icrxknvsngkrx*snkcc*ixkklnsilxi*xyifflkkkkkxkkkkkkkek
kkkkkekkkkkkn*int*ikkk*l*kkk


Frame B:
GDEFLIIKRGVENVDHADHFISQFTKNVSSSSFTVDGESSSTIFPIFFSXGGVVFKKXET
KVSSIIKSADXKMYQMEKGISQINVVEFXKN*iqf*xykxifff*kkkkkxkkkkkkkkk
kkkkkkkkkkkkik*ihk*kkndykkk


Frame C:
vmnf*slkevlkmlimliisfhnslktslqvaslstvnqvqpffqfsfxmvvlslknxkl
kflqllnlpmxkcikwkkxlvk*mllnlxkikfnfkxixiyfffkkkkkkxkkkkkkrkk
kkkkrkkkkkkklnkyinkkkmiikkk


own update 2004. 6.10
Homology vs CSM-cDNA
Query= Contig-U06349-1 (Contig-U06349-1Q)
/CSM_Contig/Contig-U06349-1Q.Seq.d
(444 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U06349-1 (Contig-U06349-1Q) /CSM_Contig/Conti... 525 e-149
Contig-U14497-1 (Contig-U14497-1Q) /CSM_Contig/Conti... 36 0.031
Contig-U14378-1 (Contig-U14378-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U12400-1 (Contig-U12400-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U11299-1 (Contig-U11299-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U06473-1 (Contig-U06473-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U12425-1 (Contig-U12425-1Q) /CSM_Contig/Conti... 32 0.48
Contig-U11694-1 (Contig-U11694-1Q) /CSM_Contig/Conti... 32 0.48
Contig-U11327-1 (Contig-U11327-1Q) /CSM_Contig/Conti... 32 0.48
Contig-U10149-1 (Contig-U10149-1Q) /CSM_Contig/Conti... 32 0.48

>Contig-U06349-1 (Contig-U06349-1Q) /CSM_Contig/Contig-U06349-1Q.Seq.d
Length = 444

Score = 525 bits (265), Expect = e-149
Identities = 298/304 (98%)
Strand = Plus / Plus


Query: 1 tggtgatgaatttttaatcattaaaagaggtgttgaaaatgttgatcatgctgatcattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 tggtgatgaatttttaatcattaaaagaggtgttgaaaatgttgatcatgctgatcattt 60


Query: 61 catttcacaattcactaaaaacgtctcttcaagtagcttcactgtcgacggtgaatcaag 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 catttcacaattcactaaaaacgtctcttcaagtagcttcactgtcgacggtgaatcaag 120


Query: 121 ttcaaccatttttccaattttcttttcanatggtggtgttgtctttaaaaaatntgaaac 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ttcaaccatttttccaattttcttttcanatggtggtgttgtctttaaaaaatntgaaac 180


Query: 181 taaagtttcttcaattattaaatctgccgatgnaaaaatgtatcaaatggaaaaaggnat 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 taaagtttcttcaattattaaatctgccgatgnaaaaatgtatcaaatggaaaaaggnat 240


Query: 241 tagtcaaataaatgttgttgaatttgnnnnnnnttaaattcaattttaaanatataaana 300
||||||||||||||||||||||||||| |||||||||||||||||||||||||||
Sbjct: 241 tagtcaaataaatgttgttgaatttgnaaaaaattaaattcaattttaaanatataaana 300


Query: 301 tata 304
||||
Sbjct: 301 tata 304


>Contig-U14497-1 (Contig-U14497-1Q) /CSM_Contig/Contig-U14497-1Q.Seq.d
Length = 1748

Score = 36.2 bits (18), Expect = 0.031
Identities = 18/18 (100%)
Strand = Plus / Minus


Query: 1 tggtgatgaatttttaat 18
||||||||||||||||||
Sbjct: 807 tggtgatgaatttttaat 790


>Contig-U14378-1 (Contig-U14378-1Q) /CSM_Contig/Contig-U14378-1Q.Seq.d
Length = 1242

Score = 34.2 bits (17), Expect = 0.12
Identities = 17/17 (100%)
Strand = Plus / Minus


Query: 249 taaatgttgttgaattt 265
|||||||||||||||||
Sbjct: 495 taaatgttgttgaattt 479


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: 5177
Number of Sequences: 6905
Number of extensions: 5177
Number of successful extensions: 660
Number of sequences better than 10.0: 229
length of query: 444
length of database: 5,674,871
effective HSP length: 16
effective length of query: 428
effective length of database: 5,564,391
effective search space: 2381559348
effective search space used: 2381559348
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 2008.11. 8
Homology vs DNA
Query= Contig-U06349-1 (Contig-U06349-1Q) /CSM_Contig/Contig-U06349-1Q.Seq.d
(444 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

(AU261941) Dictyostelium discoideum vegetative cDNA clone:VS... 561 e-156 1
(CP000387) Streptococcus sanguinis SK36, complete genome. 48 0.27 1
(EJ021777) 1095448006500 Global-Ocean-Sampling_GS-26-01-01-1... 40 0.49 2
(AP010446) Lotus japonicus genomic DNA, chromosome 5, clone:... 34 0.58 2
(AP010444) Lotus japonicus genomic DNA, chromosome 5, clone:... 34 0.60 2
(AC135392) Rattus norvegicus clone CH230-44D9, *** SEQUENCIN... 46 1.0 1
(AC130012) Rattus norvegicus clone CH230-517E12, WORKING DRA... 46 1.0 1
(AC129721) Rattus norvegicus clone CH230-42J3, WORKING DRAFT... 46 1.0 1
(AC094479) Rattus norvegicus clone CH230-4J17, WORKING DRAFT... 46 1.0 1
(AC176092) Strongylocentrotus purpuratus clone R3-24C18, WOR... 46 1.0 1
(DH705503) Rattus norvegicus DNA, BAC clone: RNB1-267E19, 5'... 46 1.0 1
(BH163023) ENTRD42TF Entamoeba histolytica Sheared DNA Entam... 38 1.6 2
(EK215748) 1095460118138 Global-Ocean-Sampling_GS-31-01-01-1... 38 1.6 2
(AC178100) Strongylocentrotus purpuratus clone R3-3068H2, WO... 44 1.8 3
(AC022690) Homo sapiens chromosome 8, clone RP11-480O10, com... 40 2.2 3
(AC181732) Strongylocentrotus purpuratus clone R3-1038A09, W... 36 2.2 4
(DW283988) UI-S-HH0-adx-l-20-0-UI.s1 UI-S-HH0 Euprymna scolo... 32 2.8 2
(CV674226) RET7SJ_30B12.T7 Schistosoma japonicum reverse cDN... 40 3.4 2
(CV672353) sjm001_B08_sjm001B08-T3 Schistosoma japonicum rev... 40 3.5 2
(AY808623) Schistosoma japonicum SJCHGC07752 protein mRNA, p... 40 3.5 2
(AC026441) Homo sapiens chromosome 5 clone CTD-2280O3, compl... 38 3.5 3
(BX255954) Zebrafish DNA sequence from clone CH211-275D2 in ... 38 3.7 2
(AC016648) Homo sapiens chromosome 5 clone RPCI-1_137K24, co... 38 4.1 3
(AC145959) Gallus gallus chromosome UNK clone CH261-17M10, c... 44 4.1 1
(BV612136) S217P61612RC7.T0 Noemie Pan troglodytes troglodyt... 44 4.1 1
(AY206774) Runaria reducta 16S ribosomal RNA gene, partial s... 44 4.1 1
(AC149952) Strongylocentrotus purpuratus clone R3-32B16, WOR... 44 4.1 1
(AC201117) Strongylocentrotus purpuratus clone R3-13N6, WORK... 44 4.1 1
(AC180970) Strongylocentrotus purpuratus clone R3-3059B02, W... 44 4.1 1
(AC180381) Strongylocentrotus purpuratus clone R3-3113H8, WO... 44 4.1 1
(AC180296) Strongylocentrotus purpuratus clone R3-3119I18, W... 44 4.1 1
(AC179557) Strongylocentrotus purpuratus clone R3-8C8, WORKI... 44 4.1 1
(AC179524) Strongylocentrotus purpuratus clone R3-1035D21, W... 44 4.1 1
(AC179321) Strongylocentrotus purpuratus clone R3-57C9, WORK... 44 4.1 1
(AC178434) Strongylocentrotus purpuratus clone R3-3041B5, WO... 44 4.1 1
(AC176568) Strongylocentrotus purpuratus clone R3-3076M7, WO... 44 4.1 1
(ET437875) ONBBD20_Reverse Onion BAC Library Allium cepa gen... 44 4.1 1
(EK043991) 1092959539498 Global-Ocean-Sampling_GS-31-01-01-1... 44 4.1 1
(EJ829816) 1093017576553 Global-Ocean-Sampling_GS-30-02-01-1... 44 4.1 1
(EJ805138) 1093017454249 Global-Ocean-Sampling_GS-30-02-01-1... 44 4.1 1
(EJ770900) 1092966607838 Global-Ocean-Sampling_GS-30-02-01-1... 44 4.1 1
(EJ740166) 1092962011848 Global-Ocean-Sampling_GS-30-02-01-1... 44 4.1 1
(EJ734552) 1092961082326 Global-Ocean-Sampling_GS-30-02-01-1... 44 4.1 1
(EJ724623) 1092959487318 Global-Ocean-Sampling_GS-30-02-01-1... 44 4.1 1
(CG754663) P050-1-F10.za Ppa EcoRI BAC Library Pristionchus ... 44 4.1 1
(EG612332) REPROTRACTF095448J11 POSSUM_01-POSSUM-C-REPROTRAC... 44 4.1 1
(EC281616) BRAINF089465F8 POSSUM_01-POSSUM-C-BRAIN-2KB Trich... 44 4.1 1
(DY774601) Sf1F02128-3-1 Spodoptera frugiperda Fat Body cDNA... 44 4.1 1
(BG935868) SS1-0195 Atlantic Salmon spleen Salmo salar cDNA ... 44 4.1 1
(CV247727) WS01119.B21_C07 PT-P-FL-A-2 Populus trichocarpa c... 38 4.8 2
(AC120413) Mus musculus chromosome 5, clone RP24-458L16, com... 38 6.5 3
(BX004858) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 38 6.7 2
(AP009180) Candidatus Carsonella ruddii PV DNA, complete gen... 30 7.6 2
(ED800926) MG__Ba0009L22r MG__Ba Mimulus guttatus genomic, g... 34 8.0 2
(EF457753) Gossypium hirsutum retrotransposon putative copia... 36 8.1 4
(AL731703) Mouse DNA sequence from clone RP23-100O16 on chro... 38 8.2 3

>(AU261941) Dictyostelium discoideum vegetative cDNA clone:VSB305,
3' end single read.
Length = 445

Score = 561 bits (283), Expect = e-156
Identities = 304/304 (100%)
Strand = Plus / Plus


Query: 1 tggtgatgaatttttaatcattaaaagaggtgttgaaaatgttgatcatgctgatcattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 tggtgatgaatttttaatcattaaaagaggtgttgaaaatgttgatcatgctgatcattt 60


Query: 61 catttcacaattcactaaaaacgtctcttcaagtagcttcactgtcgacggtgaatcaag 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 catttcacaattcactaaaaacgtctcttcaagtagcttcactgtcgacggtgaatcaag 120


Query: 121 ttcaaccatttttccaattttcttttcanatggtggtgttgtctttaaaaaatntgaaac 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ttcaaccatttttccaattttcttttcanatggtggtgttgtctttaaaaaatntgaaac 180


Query: 181 taaagtttcttcaattattaaatctgccgatgnaaaaatgtatcaaatggaaaaaggnat 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 taaagtttcttcaattattaaatctgccgatgnaaaaatgtatcaaatggaaaaaggnat 240


Query: 241 tagtcaaataaatgttgttgaatttgnaaaaaattaaattcaattttaaanatataaana 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 tagtcaaataaatgttgttgaatttgnaaaaaattaaattcaattttaaanatataaana 300


Query: 301 tata 304
||||
Sbjct: 301 tata 304

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 92845959
Number of Hits to DB: 420,737,442
Number of extensions: 28912484
Number of successful extensions: 2268161
Number of sequences better than 10.0: 56
Length of query: 444
Length of database: 95,242,211,685
Length adjustment: 23
Effective length of query: 421
Effective length of database: 93,106,754,628
Effective search space: 39197943698388
Effective search space used: 39197943698388
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 6.21
Homology vs Protein
Query= Contig-U06349-1 (Contig-U06349-1Q) /CSM_Contig/Contig-U06349-1Q.Seq.d
(444 letters)

Database: nrp_A
3,204,285 sequences; 1,040,966,779 total letters

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

Score E
Sequences producing significant alignments: (bits) Value

CP000555_2656(CP000555|pid:none) Methylibium petroleiphilum PM1,... 40 0.025
CP000961_687(CP000961|pid:none) Shewanella woodyi ATCC 51908, co... 37 0.28
AY204432_1(AY204432|pid:none) Leptospirillum ferrooxidans Lfe189... 35 1.0
CP000076_5572(CP000076|pid:none) Pseudomonas fluorescens Pf-5, c... 34 1.4
FM954973_315(FM954973|pid:none) Vibrio splendidus LGP32 chromoso... 33 2.3
CP000828_2224(CP000828|pid:none) Acaryochloris marina MBIC11017,... 33 3.0
AM181176_5475(AM181176|pid:none) Pseudomonas fluorescens SBW25 c... 33 4.0
AE004091_577(AE004091|pid:none) Pseudomonas aeruginosa PAO1, com... 33 4.0
FM209186_572(FM209186|pid:none) Pseudomonas aeruginosa LESB58 co... 33 4.0

>CP000555_2656(CP000555|pid:none) Methylibium petroleiphilum PM1,
complete genome.
Length = 1063

Score = 40.0 bits (92), Expect = 0.025
Identities = 23/79 (29%), Positives = 35/79 (44%)
Frame = +2

Query: 2 GDEFLIIKRGVENVDHADHFISQFTKNVSSSSFTVDGEXXXXXXXXXXXXGGVVFKKXET 181
GDEF+I+ GV+++D H + Q + V+G G VF T
Sbjct: 708 GDEFVIVLNGVQHIDEVTHIVDQRLIPLIRQPHLVEG----AELHVSCSVGIAVFPDDAT 763

Query: 182 KVSSIIKSADXKMYQMEKG 238
+ ++K AD MYQ + G
Sbjct: 764 DIDELMKHADTAMYQAKAG 782

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: 3204285
Number of Hits to DB: 304,640,760
Number of extensions: 3646097
Number of successful extensions: 7903
Number of sequences better than 10.0: 9
Number of HSP's gapped: 7903
Number of HSP's successfully gapped: 9
Length of query: 148
Length of database: 1,040,966,779
Length adjustment: 110
Effective length of query: 38
Effective length of database: 688,495,429
Effective search space: 26162826302
Effective search space used: 26162826302
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: 29 (15.8 bits)

PSORT

psg: 0.57 gvh: 0.36 alm: 0.40 top: 0.53 tms: 0.00 mit: 0.18 mip: 0.00
nuc: 0.00 erl: 0.00 erm: 0.20 pox: 0.00 px2: 0.00 vac: 0.00 rnp: 0.00
act: 0.00 caa: 0.00 yqr: 0.00 tyr: 0.00 leu: 0.00 gpi: 0.00 myr: 0.00
dna: 0.00 rib: 0.00 bac: 0.00 m1a: 0.00 m1b: 0.00 m2 : 0.00 mNt: 0.00
m3a: 0.00 m3b: 0.00 m_ : 1.00

56.0 %: cytoplasmic
32.0 %: nuclear
4.0 %: cytoskeletal
4.0 %: mitochondrial
4.0 %: peroxisomal

>> prediction for Contig-U06349-1 is cyt

VS (DIR, S) 1
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 0
SL (DIR, L) 0
SS (DIR, S) 0
SH (FL, L) 0
SF (FL, S) 0
CH (FL, L) 0
CF (FL, S) 0
FCL (DIR, L) 0
FC (DIR, S) 0
FC-IC (SUB) 0