Contig-U02400-1
Contig ID Contig-U02400-1
Contig update 2001. 8.29
Contig sequence
>Contig-U02400-1 (Contig-U02400-1Q) /CSM_Contig/Contig-U02400-1Q.Seq.d
TTGTCTCTAAAATGGAGGATACTTTAAAGAGACCAGAATTAATTGAAAAG
ATTAAATTATTAAATAAGAGAAAAGTTGGACCAAAGATTATAGGTTGGTT
ACAACAACATCTATTGAATGCCATTGTAATTAGAACCAAAGAAAAGAATA
ATCCAAGCTTTACACTCTATCCATTGCTTTATGAAGGCGAGTGTGATGGT
GAAAACTTTAACAATTTGGCCAATGTTAGACAAATCTTTTCATTATTAAA
ATTTGGACTTCCAACATCTAGAAATGGTTTCTACACAATCTCTTCATTAA
AAAACTATTCAACCAATTATTTAACTGCAATCTATGAAACCATTAAAGAG
GCTTTAGAACAACAAACATTAGAAATTCAACAAAAAGAATTAAAAAAACA
ACAAAGAAAATTACAACCAAAACAACCAAGATCCAAAATA

Gap no gap
Contig length 440
Chromosome number (1..6, M) 4
Chromosome length 5430582
Start point 5250692
End point 5251132
Strand (PLUS/MINUS) PLUS
Number of clones 1
Number of EST 1
Link to clone list U02400
List of clone(s)

est1=AFA844F,1,441
Translated Amino Acid sequence
VSKMEDTLKRPELIEKIKLLNKRKVGPKIIGWLQQHLLNAIVIRTKEKNNPSFTLYPLLY
EGECDGENFNNLANVRQIFSLLKFGLPTSRNGFYTISSLKNYSTNYLTAIYETIKEALEQ
QTLEIQQKELKKQQRKLQPKQPRSKI


Translated Amino Acid sequence (All Frames)
Frame A:
lslkwril*rdqn*lkrlny*irekldqrl*vgynniy*mpl*lepkkriiqalhsihcf
mkasvmvktltiwpmldksfhy*nldfqhlemvstqslh*ktiqpii*lqsmkplkrl*n
nkh*kfnkkn*knnkenynqnnqdpk


Frame B:
cl*nggyfketrin*kd*iik*ekswtkdyrlvtttsiechcn*nqrke*sklytlsial
*rrv*w*kl*qfgqc*tnlfiikiwtsni*kwflhnlfikklfnqlfncnl*nh*rgfrt
tnirnstkrikkttkkittkttkiqn


Frame C:
VSKMEDTLKRPELIEKIKLLNKRKVGPKIIGWLQQHLLNAIVIRTKEKNNPSFTLYPLLY
EGECDGENFNNLANVRQIFSLLKFGLPTSRNGFYTISSLKNYSTNYLTAIYETIKEALEQ
QTLEIQQKELKKQQRKLQPKQPRSKI


own update 2004. 6. 9
Homology vs CSM-cDNA
Query= Contig-U02400-1 (Contig-U02400-1Q)
/CSM_Contig/Contig-U02400-1Q.Seq.d
(440 letters)

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


Score E
Sequences producing significant alignments: (bits) Value

Contig-U02400-1 (Contig-U02400-1Q) /CSM_Contig/Conti... 700 0.0
Contig-U11167-1 (Contig-U11167-1Q) /CSM_Contig/Conti... 36 0.030
Contig-U11036-1 (Contig-U11036-1Q) /CSM_Contig/Conti... 36 0.030
Contig-U10835-1 (Contig-U10835-1Q) /CSM_Contig/Conti... 36 0.030
Contig-U05020-1 (Contig-U05020-1Q) /CSM_Contig/Conti... 36 0.030
Contig-U01107-1 (Contig-U01107-1Q) /CSM_Contig/Conti... 36 0.030
Contig-U13267-1 (Contig-U13267-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U12341-1 (Contig-U12341-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U12060-1 (Contig-U12060-1Q) /CSM_Contig/Conti... 34 0.12
Contig-U11258-1 (Contig-U11258-1Q) /CSM_Contig/Conti... 34 0.12

>Contig-U02400-1 (Contig-U02400-1Q) /CSM_Contig/Contig-U02400-1Q.Seq.d
Length = 440

Score = 700 bits (353), Expect = 0.0
Identities = 353/353 (100%)
Strand = Plus / Plus


Query: 1 ttgtctctaaaatggaggatactttaaagagaccagaattaattgaaaagattaaattat 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ttgtctctaaaatggaggatactttaaagagaccagaattaattgaaaagattaaattat 60


Query: 61 taaataagagaaaagttggaccaaagattataggttggttacaacaacatctattgaatg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 taaataagagaaaagttggaccaaagattataggttggttacaacaacatctattgaatg 120


Query: 121 ccattgtaattagaaccaaagaaaagaataatccaagctttacactctatccattgcttt 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ccattgtaattagaaccaaagaaaagaataatccaagctttacactctatccattgcttt 180


Query: 181 atgaaggcgagtgtgatggtgaaaactttaacaatttggccaatgttagacaaatctttt 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 atgaaggcgagtgtgatggtgaaaactttaacaatttggccaatgttagacaaatctttt 240


Query: 241 cattattaaaatttggacttccaacatctagaaatggtttctacacaatctcttcattaa 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 cattattaaaatttggacttccaacatctagaaatggtttctacacaatctcttcattaa 300


Query: 301 aaaactattcaaccaattatttaactgcaatctatgaaaccattaaagaggct 353
|||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 aaaactattcaaccaattatttaactgcaatctatgaaaccattaaagaggct 353


Score = 83.8 bits (42), Expect = 1e-16
Identities = 42/42 (100%)
Strand = Plus / Plus


Query: 399 caacaaagaaaattacaaccaaaacaaccaagatccaaaata 440
||||||||||||||||||||||||||||||||||||||||||
Sbjct: 399 caacaaagaaaattacaaccaaaacaaccaagatccaaaata 440


>Contig-U11167-1 (Contig-U11167-1Q) /CSM_Contig/Contig-U11167-1Q.Seq.d
Length = 1744

Score = 36.2 bits (18), Expect = 0.030
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 29 gagaccagaattaattga 46
||||||||||||||||||
Sbjct: 1077 gagaccagaattaattga 1094


>Contig-U11036-1 (Contig-U11036-1Q) /CSM_Contig/Contig-U11036-1Q.Seq.d
Length = 1347

Score = 36.2 bits (18), Expect = 0.030
Identities = 18/18 (100%)
Strand = Plus / Plus


Query: 234 atcttttcattattaaaa 251
||||||||||||||||||
Sbjct: 1075 atcttttcattattaaaa 1092


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: 8027
Number of Sequences: 6905
Number of extensions: 8027
Number of successful extensions: 896
Number of sequences better than 10.0: 289
length of query: 440
length of database: 5,674,871
effective HSP length: 16
effective length of query: 424
effective length of database: 5,564,391
effective search space: 2359301784
effective search space used: 2359301784
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 2009. 5.17
Homology vs DNA
Query= Contig-U02400-1 (Contig-U02400-1Q) /CSM_Contig/Contig-U02400-1Q.Seq.d
(440 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

(BJ325801) Dictyostelium discoideum cDNA clone:dda2h12, 5' e... 704 0.0 1
(AC189293) Brassica rapa subsp. pekinensis clone KBrB026F03,... 42 0.050 2
(AC232518) Brassica rapa subsp. pekinensis clone KBrB071A06,... 42 0.13 3
(AX344555) Sequence 6 from Patent WO0200932. 40 0.32 7
(FP016016) Zebrafish DNA sequence from clone CH1073-78H13 in... 46 1.1 1
(AL954649) Zebrafish DNA sequence from clone CH211-285P11. 46 1.1 1
(AL670708) Mouse DNA sequence from clone RP23-125A21 on chro... 46 1.1 1
(CU457732) S.lycopersicum DNA sequence from clone LE_HBa-182... 46 1.1 1
(AC215840) Populus trichocarpa clone POP043-C12, complete se... 46 1.1 1
(CR926470) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 1.1 1
(CR926465) Zebrafish DNA sequence *** SEQUENCING IN PROGRESS... 46 1.1 1
(AC232690) Solanum lycopersicum chromosome 0 clone C00Hba023... 46 1.1 1
(EK108294) 1092963075330 Global-Ocean-Sampling_GS-31-01-01-1... 46 1.1 1
(BA000016) Clostridium perfringens str. 13 DNA, complete gen... 46 1.1 1
(BV943281) pRRL2:Newb:20080411:323148 USMARC Pig Breed SNP D... 40 1.7 2
(EI959728) SB_BBc144-E07.F SB_BBc Sorghum bicolor genomic 5'... 32 2.9 2
(CV754798) sjl4-005B01-T7_009.ab1 SJL Schistosoma japonicum ... 34 3.0 2
(AC113289) Mus musculus chromosome 15, clone RP23-414M11, co... 44 4.4 1
(DL268749) METHODS FOR ANALYZING GENES OF INDUSTRIAL YEASTS. 44 4.4 1
(DJ135198) Method for identification of useful proteins deri... 44 4.4 1
(AC169231) Bos taurus clone CH240-216M9, WORKING DRAFT SEQUE... 44 4.4 1
(EK104927) 1092963042758 Global-Ocean-Sampling_GS-31-01-01-1... 44 4.4 1
(AM632805) Entamoeba dispar GSS, clone dispar94f07.p1k. 44 4.4 1
(AM630427) Entamoeba dispar GSS, clone dispar55e11.p1k. 44 4.4 1
(AM628542) Entamoeba dispar GSS, clone dispar29g10.q1k. 44 4.4 1
(DX573383) Phaseolus-Bat-7_02_K05.F Phaseolus-Bat-7 Phaseolu... 44 4.4 1
(DX459998) Cpl01654 Papaya Genomic DNA BAC Library Carica pa... 44 4.4 1
(DU887966) 389444 Tomato HindIII BAC Library Solanum lycoper... 44 4.4 1
(CJ446372) Macaca fascicularis mRNA, clone: QflA-11658, 5' e... 44 4.4 1
(CP000300) Methanococcoides burtonii DSM 6242, complete genome. 44 4.4 1
(AC168926) Bos taurus clone CH240-233N6, WORKING DRAFT SEQUE... 40 4.4 2
(CU104783) Zebrafish DNA sequence from clone CH73-43P17 in l... 40 4.7 3
(EK312073) 1095462400569 Global-Ocean-Sampling_GS-31-01-01-1... 40 5.1 2
(AY583235) Mycoplasma fermentans strain PG18 putative transp... 32 5.3 4
(EK538266) 1095516042001 Global-Ocean-Sampling_GS-32-01-01-1... 36 5.8 2
(EK403642) 1095469554185 Global-Ocean-Sampling_GS-31-01-01-1... 34 5.9 2
(AC221915) Bos taurus clone CH240-378B17, WORKING DRAFT SEQU... 38 6.7 4
(AC221914) Bos taurus clone CH240-378B13, WORKING DRAFT SEQU... 38 6.8 3
(AC018922) Homo sapiens 12 BAC RP11-485C17 (Roswell Park Can... 36 7.0 3

>(BJ325801) Dictyostelium discoideum cDNA clone:dda2h12, 5' end,
single read.
Length = 441

Score = 704 bits (355), Expect = 0.0
Identities = 355/355 (100%)
Strand = Plus / Plus


Query: 1 ttgtctctaaaatggaggatactttaaagagaccagaattaattgaaaagattaaattat 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 1 ttgtctctaaaatggaggatactttaaagagaccagaattaattgaaaagattaaattat 60


Query: 61 taaataagagaaaagttggaccaaagattataggttggttacaacaacatctattgaatg 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 61 taaataagagaaaagttggaccaaagattataggttggttacaacaacatctattgaatg 120


Query: 121 ccattgtaattagaaccaaagaaaagaataatccaagctttacactctatccattgcttt 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 121 ccattgtaattagaaccaaagaaaagaataatccaagctttacactctatccattgcttt 180


Query: 181 atgaaggcgagtgtgatggtgaaaactttaacaatttggccaatgttagacaaatctttt 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 181 atgaaggcgagtgtgatggtgaaaactttaacaatttggccaatgttagacaaatctttt 240


Query: 241 cattattaaaatttggacttccaacatctagaaatggtttctacacaatctcttcattaa 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 241 cattattaaaatttggacttccaacatctagaaatggtttctacacaatctcttcattaa 300


Query: 301 aaaactattcaaccaattatttaactgcaatctatgaaaccattaaagaggcttt 355
|||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 301 aaaactattcaaccaattatttaactgcaatctatgaaaccattaaagaggcttt 355

Lambda K H
1.37 0.711 1.31

Matrix: blastn matrix:1 -3
Number of Sequences: 102105510
Number of Hits to DB: 503,835,070
Number of extensions: 31476557
Number of successful extensions: 2443258
Number of sequences better than 10.0: 39
Length of query: 440
Length of database: 101,790,757,118
Length adjustment: 23
Effective length of query: 417
Effective length of database: 99,442,330,388
Effective search space: 41467451771796
Effective search space used: 41467451771796
X1: 11 (21.8 bits)
S2: 21 (42.1 bits)

protein update 2009. 7.19
Homology vs Protein
Query= Contig-U02400-1 (Contig-U02400-1Q) /CSM_Contig/Contig-U02400-1Q.Seq.d
(440 letters)

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

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

Score E
Sequences producing significant alignments: (bits) Value

CP001618_1342(CP001618|pid:none) Beutenbergia cavernae DSM 12333... 35 1.1
(B0YPN0) RecName: Full=Maturase K; AltName: Full=Intron maturase... 32 9.0

>CP001618_1342(CP001618|pid:none) Beutenbergia cavernae DSM 12333,
complete genome.
Length = 626

Score = 34.7 bits (78), Expect = 1.1
Identities = 28/83 (33%), Positives = 43/83 (51%), Gaps = 3/83 (3%)
Frame = +3

Query: 27 KRPELIEKIKLLNKRKVGPKIIGWLQQHLLNAIVIRTKEKNNP---SFTLYPLLYEGECD 197
K P+L + ++ R + P+ + ++ HL + E+ NP SF YP+L EGE D
Sbjct: 356 KLPDLAIVLDII--RSIDPECLPYVN-HLPGFDYVEAVEQTNPEVLSFDRYPILLEGE-D 411

Query: 198 GENFNNLANVRQIFSLLKFGLPT 266
F N A+VR + L G+PT
Sbjct: 412 AGYFRNWADVRA--AALPGGIPT 432

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: 611,653,075
Number of extensions: 10292059
Number of successful extensions: 22504
Number of sequences better than 10.0: 2
Number of HSP's gapped: 22502
Number of HSP's successfully gapped: 2
Length of query: 146
Length of database: 1,051,180,864
Length adjustment: 109
Effective length of query: 37
Effective length of database: 698,395,933
Effective search space: 25840649521
Effective search space used: 25840649521
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: 0.49 gvh: 0.40 alm: 0.46 top: 0.53 tms: 0.00 mit: 0.19 mip: 0.00
nuc: 0.06 erl: 0.00 erm: 0.20 pox: 0.30 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
16.0 %: nuclear
12.0 %: mitochondrial
8.0 %: cytoskeletal
8.0 %: peroxisomal

>> prediction for Contig-U02400-1 is cyt

VS (DIR, S) 0
VH (FL, L) 0
VF (FL, S) 0
AH (FL, L) 0
AF (FL, S) 1
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